From ca12caac10d7caa065441003ccf65b030849aa45 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Tue, 12 Jan 2021 16:49:21 +0100
Subject: [PATCH 01/64] evaluation against BioNLP-OST 2019 BB using
 entities.plan

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 create mode 100644 process-evaluate_BioNLP-OST.snakefile

diff --git a/.gitignore b/.gitignore
index a788b67c..09e7e901 100644
--- a/.gitignore
+++ b/.gitignore
@@ -42,6 +42,9 @@ corpora/microbes-2019/batch/*/uses.txt
 corpora/microbes-2019/batch/*/words.txt
 corpora/microbes-2019/batch/*/yatea-var/
 corpora/microbes-2019/batch/*/yatea/
+corpora/microbes-2019/expander/
+corpora/microbes-2019/*.full.txt
+corpora/microbes-2019/index/
 .snakemake/
 ancillaries/BioNLP-OST+EnovFood-Habitat.json
 ancillaries/BioNLP-OST+EnovFood-Habitat.paths
diff --git a/config/config.yaml b/config/config.yaml
index f76cb312..9b2c74a1 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -38,6 +38,9 @@ PUBMED_BATCHES_HOME : "corpora/microbes-2019/batch"
 PUBMED_HABITAT_RESULT : "ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt"
 PUBMED_PHENOTYPE_RESULT : "ancillaries/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
 
+## bionlp-ost
+BIONLPOST_BATCHES_HOME : "corpora/BioNLP-OST-2019/batch"
+BIONLPOST_API : "http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/api"
 
 ## index
 ALVISIR_INDEX : "corpora/microbes-2019/index"
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/plans/entities.plan b/plans/entities.plan
index 3a9ec07d..80138040 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -2,193 +2,208 @@
 
 <alvisnlp-plan id="entities">
 
+  <param name="format">
+    <alias module="read" param="select"/>
+  </param>
+  
   <param name="input">
-  <alias module="read" param="sourcePath"/>
+    <alias module="read.pubmed" param="sourcePath"/>
+  </param>
+  
+  <param name="input-dir">
+    <alias module="read.bionlp-st" param="textDir"/>
   </param>
 
   <param name="input-xslt">
-  <alias module="read" param="xslTransform"/>
+    <alias module="read.pubmed" param="xslTransform"/>
   </param>
 
   <param name="outputDir">
-  <alias module="output.doc-mesh" param="outDir"/>
-  <alias module="output.taxa" param="outDir"/>
-  <alias module="output.microorganisms" param="outDir"/>
-  <alias module="output.microorganisms-short" param="outDir"/>
-  <alias module="output.bacteria" param="outDir"/>
-  <alias module="output.habitats" param="outDir"/>
-  <alias module="output.phenotypes" param="outDir"/>
-  <alias module="output.uses" param="outDir"/>
-  <alias module="output.geo" param="outDir"/>
-  <alias module="output.relations" param="outDir"/>
-  <alias module="output.relations-pheno" param="outDir"/>
-  <alias module="output.relations-use" param="outDir"/>
-  <alias module="output.dependencies.sentences" param="outDir"/>
-  <alias module="output.dependencies.anaphora" param="outDir"/>
-  <alias module="output.dependencies.dependencies" param="outDir"/>
-  <alias module="words" param="outDir"/>
-  <alias module="success" param="outDir"/>
+    <alias module="output.doc-mesh" param="outDir"/>
+    <alias module="output.taxa" param="outDir"/>
+    <alias module="output.microorganisms" param="outDir"/>
+    <alias module="output.microorganisms-short" param="outDir"/>
+    <alias module="output.bacteria" param="outDir"/>
+    <alias module="output.habitats" param="outDir"/>
+    <alias module="output.phenotypes" param="outDir"/>
+    <alias module="output.uses" param="outDir"/>
+    <alias module="output.geo" param="outDir"/>
+    <alias module="output.relations" param="outDir"/>
+    <alias module="output.relations-pheno" param="outDir"/>
+    <alias module="output.relations-use" param="outDir"/>
+    <alias module="output.dependencies.sentences" param="outDir"/>
+    <alias module="output.dependencies.anaphora" param="outDir"/>
+    <alias module="output.dependencies.dependencies" param="outDir"/>
+    <alias module="words" param="outDir"/>
+    <alias module="success" param="outDir"/>
   </param>
 
   <param name="doc-mesh">
-  <alias module="output.doc-mesh" param="fileName"/>
+    <alias module="output.doc-mesh" param="fileName"/>
   </param>
 
   <param name="taxa">
-  <alias module="output.taxa" param="fileName"/>
+    <alias module="output.taxa" param="fileName"/>
   </param>
 
   <param name="microorganisms">
-  <alias module="output.microorganisms" param="fileName"/>
+    <alias module="output.microorganisms" param="fileName"/>
   </param>
 
   <param name="microorganisms-short">
-  <alias module="output.microorganisms-short" param="fileName"/>
+    <alias module="output.microorganisms-short" param="fileName"/>
   </param>
 
   <param name="bacteria">
-  <alias module="output.bacteria" param="fileName"/>
+    <alias module="output.bacteria" param="fileName"/>
   </param>
 
-   <param name="habitats">
-  <alias module="output.habitats" param="fileName"/>
-   </param>
+  <param name="habitats">
+    <alias module="output.habitats" param="fileName"/>
+  </param>
 
   <param name="phenotypes">
-  <alias module="output.phenotypes" param="fileName"/>
+    <alias module="output.phenotypes" param="fileName"/>
   </param>
 
-	<param name="uses">
-	  <alias module="output.uses" param="fileName"/>
-	</param>
-
-	<param name="geo">
-	  <alias module="output.geo" param="fileName"/>
-	</param>
-
-	<param name="relations">
-	  <alias module="output.relations" param="fileName"/>
-	</param>
-
-	<param name="relations-pheno">
-	  <alias module="output.relations-pheno" param="fileName"/>
-	</param>
-
-	<param name="relations-use">
-	  <alias module="output.relations-use" param="fileName"/>
-	</param>
-
-	<param name="sentences">
-	  <alias module="output.dependencies.sentences" param="fileName"/>
-	</param>
-
-	<param name="anaphora">
-	  <alias module="output.dependencies.anaphora" param="fileName"/>
-	</param>
-
-	<param name="dependencies">
-	  <alias module="output.dependencies.dependencies" param="fileName"/>
-	</param>
+  <param name="uses">
+    <alias module="output.uses" param="fileName"/>
+  </param>
+  
+  <param name="geo">
+    <alias module="output.geo" param="fileName"/>
+  </param>
+  
+  <param name="relations">
+    <alias module="output.relations" param="fileName"/>
+  </param>
 
-	<param name="words">
-	  <alias module="words" param="fileName"/>
-	</param>
+  <param name="relations-pheno">
+    <alias module="output.relations-pheno" param="fileName"/>
+  </param>
 
+  <param name="relations-use">
+    <alias module="output.relations-use" param="fileName"/>
+  </param>
+  
+  <param name="sentences">
+    <alias module="output.dependencies.sentences" param="fileName"/>
+  </param>
+  
+  <param name="anaphora">
+    <alias module="output.dependencies.anaphora" param="fileName"/>
+  </param>
+  
+  <param name="dependencies">
+    <alias module="output.dependencies.dependencies" param="fileName"/>
+  </param>
+  
+  <param name="words">
+    <alias module="words" param="fileName"/>
+  </param>
+  
   <param name="success">
-  <alias module="success" param="fileName"/>
+    <alias module="success" param="fileName"/>
   </param>
 
- <param name="2017MeshTree">
-  <alias module="mesh-path" param="mappingFile"/>
+  <param name="2017MeshTree">
+    <alias module="mesh-path" param="mappingFile"/>
   </param>
 
- <param name="stopwords_EN">
-  <alias module="stopwordsprojector" param="dictFile"/>
+  <param name="stopwords_EN">
+    <alias module="stopwordsprojector" param="dictFile"/>
   </param>
 
- <param name="microorganism_stopwords">
-  <alias module="stopwordsprojector-microorganism" param="dictFile"/>
+  <param name="microorganism_stopwords">
+    <alias module="stopwordsprojector-microorganism" param="dictFile"/>
   </param>
 
- <param name="food-process-lexicon">
-  <alias module="dict" param="dictFile"/>
+  <param name="food-process-lexicon">
+    <alias module="dict" param="dictFile"/>
   </param>
 
- <!--param name="noun_adj_and_spelling_variants">
-  <alias module="term-extraction.variant-projection" param="dictFile"/>
-  </param-->
+  <!--param name="noun_adj_and_spelling_variants">
+      <alias module="term-extraction.variant-projection" param="dictFile"/>
+      </param-->
 
   <param name="taxid_microorganisms">
-  <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
-  <alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
+    <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
+    <alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
   </param>
 
   <param name="taxa+id_full">
-  <alias module="taxa.dict" param="dictFile"/>
+    <alias module="taxa.dict" param="dictFile"/>
   </param>
 
 
   <param name="NCBI_taxa_ontobiotope">
-   <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
+    <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
   </param>
 
 
-<!-- habitats-->
-   <param name="ontobiotope-habitat">
-   <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-on-variants.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.concept-path" param="oboFiles"/> 
+  <!-- habitats-->
+  <param name="ontobiotope-habitat">
+    <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-on-variants.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.concept-path" param="oboFiles"/> 
   </param>
 
   <param name="ontobiotope-tomap-habitat">
-   <alias module="habitats.tomap-habitats.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
   </param>
 
-<!-- phenotypes-->
-   <param name="ontobiotope-phenotypes">
-   <alias module="tomap-phenotypes.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-on-variants.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.concept-path" param="oboFiles"/> 
+  <!-- phenotypes-->
+  <param name="ontobiotope-phenotypes">
+    <alias module="tomap-phenotypes.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-on-variants.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.concept-path" param="oboFiles"/> 
   </param>
 
   <param name="ontobiotope-tomap-phenotypes">
-   <alias module="tomap-phenotypes.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
   </param>
 
-<!-- use-->
-   <param name="ontobiotope-use">
-   <alias module="use.exact-match" param="oboFiles"/>
-   <alias module="use.exact-match-2" param="oboFiles"/>
+  <!-- use-->
+  <param name="ontobiotope-use">
+    <alias module="use.exact-match" param="oboFiles"/>
+    <alias module="use.exact-match-2" param="oboFiles"/>
   </param>
 
-<!-- mono anaphora-->
-   <param name="anaphoraLexicon">
-   <alias module="anaphora.anaphora-plan.coreferences.mono-anaphora.anaphora" param="dictFile"/>
+  <!-- mono anaphora-->
+  <param name="anaphoraLexicon">
+    <alias module="anaphora.anaphora-plan.coreferences.mono-anaphora.anaphora" param="dictFile"/>
   </param>
 
-<!-- multi anaphora-->
-   <param name="biAnaphoraLexicon">
-   <alias module="anaphora.anaphora-plan.coreferences.multi-ante-anaphora.bi-anaphora" param="dictFile"/>
+  <!-- multi anaphora-->
+  <param name="biAnaphoraLexicon">
+    <alias module="anaphora.anaphora-plan.coreferences.multi-ante-anaphora.bi-anaphora" param="dictFile"/>
   </param>
 
-
-  <read class="XMLReader">
-    <sourcePath>corpora/&corpus;/batch/&batch;/batch.xml</sourcePath>
-    <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
+  <read>
+    <pubmed class="XMLReader">
+      <sourcePath>corpora/&corpus;/batch/&batch;/batch.xml</sourcePath>
+      <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
+    </pubmed>
+
+    <bionlp-st class="BioNLPSTReader">
+      <active>true</active>
+      <sectionName>abstract</sectionName>
+      <textDir>corpora/&corpus;/batch/&batch;/bionlp-st</textDir>
+    </bionlp-st>
   </read>
 
   <assert class="Assert">
@@ -210,7 +225,7 @@
     <setFeatures/>
   </set-url>
 
-<!-- Get year -->
+  <!-- Get year -->
   <set-year class="Action">
     <target>documents[@year == "" and not @date == ""]</target>
     <action>set:feat:year(str:seds(@date,"^(\\d+) .+$","$1"))</action>
@@ -220,22 +235,22 @@
   <taxa file="plans/taxa.plan"/>
 
 
-<!-- Project stopwords -->
-<stopwordsprojector class="TabularProjector">
-  <dictFile>ancillaries/stopwords_EN.txt</dictFile>
-  <targetLayerName>stopwords</targetLayerName>
-  <valueFeatures>stopwords</valueFeatures>
-  <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
-  <caseInsensitive>true</caseInsensitive>
-</stopwordsprojector>
+  <!-- Project stopwords -->
+  <stopwordsprojector class="TabularProjector">
+    <dictFile>ancillaries/stopwords_EN.txt</dictFile>
+    <targetLayerName>stopwords</targetLayerName>
+    <valueFeatures>stopwords</valueFeatures>
+    <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
+    <caseInsensitive>true</caseInsensitive>
+  </stopwordsprojector>
 
-<stopwordsprojector-microorganism class="TabularProjector">
-  <dictFile>ancillaries/microorganism_stopwords.txt</dictFile>
-  <targetLayerName>microorganism-stopwords</targetLayerName>
-  <valueFeatures>stopwords</valueFeatures>
-  <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
-  <caseInsensitive>true</caseInsensitive>
-</stopwordsprojector-microorganism>
+  <stopwordsprojector-microorganism class="TabularProjector">
+    <dictFile>ancillaries/microorganism_stopwords.txt</dictFile>
+    <targetLayerName>microorganism-stopwords</targetLayerName>
+    <valueFeatures>stopwords</valueFeatures>
+    <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
+    <caseInsensitive>true</caseInsensitive>
+  </stopwordsprojector-microorganism>
 
   <geo>
     <stanford class="StanfordNER">
@@ -323,9 +338,9 @@
   <!-- Detect abbreviations -->
   <abbrev class="Ab3P">
     <!--installDir>/projet/maiage/save/textemig/projet-work/software/Ab3P-v1.5</installDir-->
-	<!-- layers: 'short-forms', 'long-forms' -->
-	<!-- in 'short-forms', feature 'long-form' -->
-	<!-- relations: 'abbreviations', roles 'short-form', 'long-form' -->
+    <!-- layers: 'short-forms', 'long-forms' -->
+    <!-- in 'short-forms', feature 'long-form' -->
+    <!-- relations: 'abbreviations', roles 'short-form', 'long-form' -->
   </abbrev>
 
   <!-- Project process lexicon -->
@@ -451,41 +466,41 @@
   <!-- Tag and normalize Use entities -->
   <use file="plans/use-extraction.plan"/>
 
-<!-- Filter entities spanning stopwords -->
-<stopwords class="Action">
-  <target>documents.sections.layer:habitats[span:stopwords] | documents.sections.layer:Geographical[span:stopwords] | documents.sections.layer:locations[span:stopwords] | documents.sections.layer:microorganism[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:bacteria[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:phenotypes[span:stopwords] | documents.sections.layer:uses[span:stopwords]</target>
-  <action>delete</action>
-  <deleteElements/>
-</stopwords>
-
- <!-- <module id="remove-microorganism-equal-to-numbers-1" class="Action"> -->
- <!--    <target>documents.sections.layer:microorganism[@form =~ "^\\d+$"]</target> -->
- <!--    <action>set:feat:to-remove(not section.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^\\d+$"])</action> -->
- <!--    <setFeatures/> -->
- <!--  </module> -->
- <!-- <module id="remove-microorganism-equal-to-numbers-2" class="Action"> -->
- <!--    <target>documents.sections.layer:microorganism[@to-remove == "true"]</target> -->
- <!--    <action>remove:microorganism</action> -->
- <!--    <removeFromLayer/> -->
- <!--  </module> -->
- <remove-short-microorganism-1 class="Action">
+  <!-- Filter entities spanning stopwords -->
+  <stopwords class="Action">
+    <target>documents.sections.layer:habitats[span:stopwords] | documents.sections.layer:Geographical[span:stopwords] | documents.sections.layer:locations[span:stopwords] | documents.sections.layer:microorganism[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:bacteria[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:phenotypes[span:stopwords] | documents.sections.layer:uses[span:stopwords]</target>
+    <action>delete</action>
+    <deleteElements/>
+  </stopwords>
+
+  <!-- <module id="remove-microorganism-equal-to-numbers-1" class="Action"> -->
+  <!--    <target>documents.sections.layer:microorganism[@form =~ "^\\d+$"]</target> -->
+  <!--    <action>set:feat:to-remove(not section.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^\\d+$"])</action> -->
+  <!--    <setFeatures/> -->
+  <!--  </module> -->
+  <!-- <module id="remove-microorganism-equal-to-numbers-2" class="Action"> -->
+  <!--    <target>documents.sections.layer:microorganism[@to-remove == "true"]</target> -->
+  <!--    <action>remove:microorganism</action> -->
+  <!--    <removeFromLayer/> -->
+  <!--  </module> -->
+  <remove-short-microorganism-1 class="Action">
     <target>documents.sections.layer:microorganism[@form =~ "^..?$"]</target>
     <action>set:feat:to-remove(not section.document.sections.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^..?$"])</action>
     <setFeatures/>
   </remove-short-microorganism-1>
- <remove-short-microorganism-2 class="Action">
+  <remove-short-microorganism-2 class="Action">
     <target>documents.sections.layer:microorganism[@to-remove == "true"]</target>
     <action>remove:microorganism</action>
     <removeFromLayer/>
   </remove-short-microorganism-2>
 
- <remove-microorganism-spanning-units class="Action">
+  <remove-microorganism-spanning-units class="Action">
     <target>documents.sections.layer:microorganism[outside:units]</target>
     <action>remove:microorganism</action>
     <removeFromLayer/>
- </remove-microorganism-spanning-units>
+  </remove-microorganism-spanning-units>
 
-<!-- Get lemmatized form -->
+  <!-- Get lemmatized form -->
   <get-CD-lemmas class="Action">
     <target>documents.sections.layer:words[@lemma == "@card@"]</target>
     <action>set:feat:lemma(@form)</action>
@@ -504,13 +519,13 @@
   </get-lemmas-for-entities-2>
 
   <!--
-  <module id="mbto-vocabulary" class="FileMapper">
-    <target>documents.sections.layer:words</target>
-    <form>@lemma</form>
-    <ignoreCase/>
-    <mappingFile>&ontobiotope;_words.txt</mappingFile>
-    <targetFeatures>mbto-word</targetFeatures>
-  </module>
+      <module id="mbto-vocabulary" class="FileMapper">
+      <target>documents.sections.layer:words</target>
+      <form>@lemma</form>
+      <ignoreCase/>
+      <mappingFile>&ontobiotope;_words.txt</mappingFile>
+      <targetFeatures>mbto-word</targetFeatures>
+      </module>
   -->
 
   <anaphora>
@@ -526,37 +541,37 @@
     <!-- XXX foodborne, soilborne, all water and soil -->
     <localization-relations>
       <triggers class="Action">
-    	<target>documents.sections.layer:words[@form =~ "^(parasit|attack|coloniz|flora|infect|inhabit|invade|important|host|environment|niche|habitat|effect|contamin|ecolog|toward|presen|subject|induce|implicate|ingest|grow|detect|found|live|spread|survive|unable|commensal|isolate|symbio|relationship|present|discover|observ|econom|disease|virulence|chronic|symptom|syndrome|severe|fever|caus|treat|prevalence|outbreak|epidem|ill|pathogen|phytopathogen|infest|ingest|fed|eat)"]</target>
-    	<action>add:triggers</action>
-    	<addToLayer/>
+	<target>documents.sections.layer:words[@form =~ "^(parasit|attack|coloniz|flora|infect|inhabit|invade|important|host|environment|niche|habitat|effect|contamin|ecolog|toward|presen|subject|induce|implicate|ingest|grow|detect|found|live|spread|survive|unable|commensal|isolate|symbio|relationship|present|discover|observ|econom|disease|virulence|chronic|symptom|syndrome|severe|fever|caus|treat|prevalence|outbreak|epidem|ill|pathogen|phytopathogen|infest|ingest|fed|eat)"]</target>
+	<action>add:triggers</action>
+	<addToLayer/>
       </triggers>
 
       <create-relation class="Action">
-    	<target>documents.sections</target>
-    	<action>new:relation:CooccurrenceLocalization</action>
-    	<createRelations/>
+	<target>documents.sections</target>
+	<action>new:relation:CooccurrenceLocalization</action>
+	<createRelations/>
       </create-relation>
 
       <create-tuples class="Action">
-      	<target>documents.sections.layer:sentences[inside:triggers]</target>
-      	<action>
-      	  inside:microorganism as b.
-      	  target.inside:locations as l.
-      	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
-      	</action>
-      	<createTuples/>
-      	<setArguments/>
+	<target>documents.sections.layer:sentences[inside:triggers]</target>
+	<action>
+	  inside:microorganism as b.
+	  target.inside:locations as l.
+	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
+	</action>
+	<createTuples/>
+	<setArguments/>
       </create-tuples>
 
       <create-tuples-anaphora class="Action">
-  	<target>documents.sections.layer:sentences[inside:triggers and not inside:microorganism]</target>
-  	<action>
-  	  inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as b.
-  	  target.inside:locations as l.
-  	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
-  	</action>
-  	<createTuples/>
-  	<setArguments/>
+	<target>documents.sections.layer:sentences[inside:triggers and not inside:microorganism]</target>
+	<action>
+	  inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as b.
+	  target.inside:locations as l.
+	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
+	</action>
+	<createTuples/>
+	<setArguments/>
       </create-tuples-anaphora>
     </localization-relations>
   </predictions>
@@ -567,37 +582,37 @@
     <deleteElements/>
   </remove-geographical-relations>
 
-<phenotype-relations>
-  <find-pattern class="PatternMatcher">
-    <pattern>
-      [outside:phenotypes]+
-      [true]{0,4}
-      ([outside:microorganism or @microorganism]+
-      [@form==","]?)+
-      ([@form=="and"]
-      [outside:microorganism or @microorganism])?
-    </pattern>
-    <actions>
-      <createAnnotation layer="phenotype-relations"/>
-    </actions>
-  </find-pattern>
-
-  <create-relation class="Action">
-    <target>documents.sections</target>
-    <action>new:relation:PhenotypeRelation</action>
-    <createRelations/>
-  </create-relation>
-
-  <create-tuple class="Action">
-    <target>documents.sections.layer:phenotype-relations[outside:sentences]</target>
-    <action>
-      target.inside:phenotypes as p.
-      target.inside:microorganism as m.
-      section.relations:PhenotypeRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Phenotype(p))
-    </action>
-    <createTuples/>
-    <setArguments/>
-  </create-tuple>
+  <phenotype-relations>
+    <find-pattern class="PatternMatcher">
+      <pattern>
+	[outside:phenotypes]+
+	[true]{0,4}
+	([outside:microorganism or @microorganism]+
+	[@form==","]?)+
+	([@form=="and"]
+	[outside:microorganism or @microorganism])?
+      </pattern>
+      <actions>
+	<createAnnotation layer="phenotype-relations"/>
+      </actions>
+    </find-pattern>
+
+    <create-relation class="Action">
+      <target>documents.sections</target>
+      <action>new:relation:PhenotypeRelation</action>
+      <createRelations/>
+    </create-relation>
+
+    <create-tuple class="Action">
+      <target>documents.sections.layer:phenotype-relations[outside:sentences]</target>
+      <action>
+	target.inside:phenotypes as p.
+	target.inside:microorganism as m.
+	section.relations:PhenotypeRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Phenotype(p))
+      </action>
+      <createTuples/>
+      <setArguments/>
+    </create-tuple>
 
     <!-- <create-tuple class="Action"> -->
     <!--   <target>documents.sections.layer:sentences</target> -->
@@ -621,15 +636,15 @@
     <!--   <setArguments/> -->
     <!-- </module> -->
 
-</phenotype-relations>
+  </phenotype-relations>
 
-<use-relations>
+  <use-relations>
 
-  <create-relation class="Action">
-    <target>documents.sections</target>
-    <action>new:relation:UseRelation</action>
-    <createRelations/>
-  </create-relation>
+    <create-relation class="Action">
+      <target>documents.sections</target>
+      <action>new:relation:UseRelation</action>
+      <createRelations/>
+    </create-relation>
 
     <create-tuple class="Action">
       <target>documents.sections.layer:sentences</target>
@@ -645,15 +660,15 @@
     <create-tuples-anaphora class="Action">
       <target>documents.sections.layer:sentences[not inside:microorganism]</target>
       <action>
-  	inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as m.
-  	target.inside:uses as p.
-  	section.relations:UseRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Use(p))
+	inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as m.
+	target.inside:uses as p.
+	section.relations:UseRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Use(p))
       </action>
       <createTuples/>
       <setArguments/>
     </create-tuples-anaphora>
 
-</use-relations>
+  </use-relations>
 
   <output>
     <doc-mesh class="TabularExport">
@@ -676,16 +691,16 @@
       <fileName>"taxa.txt"</fileName>
       <lines>documents.sections.layer:taxa</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </taxa>
 
@@ -695,16 +710,16 @@
       <fileName>"microorganisms.txt"</fileName>
       <lines>documents.sections.layer:microorganism</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </microorganisms>
 
@@ -714,16 +729,16 @@
       <fileName>"microorganisms-short.txt"</fileName>
       <lines>documents.sections.layer:microorganism[outside:words and not @form == outside:words.@form]</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </microorganisms-short>
 
@@ -733,16 +748,16 @@
       <fileName>"bacteria.txt"</fileName>
       <lines>documents.sections.layer:bacteria</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </bacteria>
 
@@ -752,18 +767,18 @@
       <fileName>"habitats.txt"</fileName>
       <lines>documents.sections.layer:habitats</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </habitats>
 
@@ -773,18 +788,18 @@
       <fileName>"phenotypes.txt"</fileName>
       <lines>documents.sections.layer:phenotypes</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </phenotypes>
 
@@ -794,18 +809,18 @@
       <fileName>"uses.txt"</fileName>
       <lines>documents.sections.layer:uses</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </uses>
 
@@ -815,11 +830,11 @@
       <fileName>"geo.txt"</fileName>
       <lines>documents.sections.layer:Geographical</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string
       </columns>
     </geo>
@@ -830,20 +845,20 @@
       <fileName>"relations.txt"</fileName>
       <lines>documents.sections.relations:CooccurrenceLocalization.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Bacterium.@taxid;
-    	args:Bacterium.@form;
-    	args:Bacterium.@lemma-string;
-    	args:Bacterium.@canonical-name;
-    	args:Bacterium.@path;
-    	args:Localization.@concept-id;
-    	args:Localization.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Bacterium.@taxid;
+	args:Bacterium.@form;
+	args:Bacterium.@lemma-string;
+	args:Bacterium.@canonical-name;
+	args:Bacterium.@path;
+	args:Localization.@concept-id;
+	args:Localization.@form;
 	args:Localization.@lemma-string;
-    	args:Localization.@concept-name;
+	args:Localization.@concept-name;
 	str:join:','(sort:nsval(args:Localization.nav:features:concept-path,@value),@value)
-    	<!-- args:Localization.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Localization.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations>
 
@@ -853,20 +868,20 @@
       <fileName>"phenotype-relations.txt"</fileName>
       <lines>documents.sections.relations:PhenotypeRelation.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Microorganism.@taxid;
-    	args:Microorganism.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Microorganism.@taxid;
+	args:Microorganism.@form;
 	args:Microorganism.@lemma-string;
-    	args:Microorganism.@canonical-name;
-    	args:Microorganism.@path;
-    	args:Phenotype.@concept-id;
-    	args:Phenotype.@form;
+	args:Microorganism.@canonical-name;
+	args:Microorganism.@path;
+	args:Phenotype.@concept-id;
+	args:Phenotype.@form;
 	args:Phenotype.@lemma-string;
-    	args:Phenotype.@concept-name;
+	args:Phenotype.@concept-name;
 	str:join:','(sort:nsval(args:Phenotype.nav:features:concept-path,@value),@value)
-    	<!-- args:Phenotype.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Phenotype.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations-pheno>
 
@@ -876,20 +891,20 @@
       <fileName>"uses-relations.txt"</fileName>
       <lines>documents.sections.relations:UseRelation.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Microorganism.@taxid;
-    	args:Microorganism.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Microorganism.@taxid;
+	args:Microorganism.@form;
 	args:Microorganism.@lemma-string;
-    	args:Microorganism.@canonical-name;
-    	args:Microorganism.@path;
-    	args:Use.@concept-id;
-    	args:Use.@form;
+	args:Microorganism.@canonical-name;
+	args:Microorganism.@path;
+	args:Use.@concept-id;
+	args:Use.@form;
 	args:Use.@lemma-string;
-    	args:Use.@concept-name;
+	args:Use.@concept-name;
 	str:join:','(sort:nsval(args:Use.nav:features:concept-path,@value),@value)
-    	<!-- args:Use.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Use.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations-use>
 
@@ -912,7 +927,7 @@
     <!-- 	| stmt:res(obta:document, pmid^section.document.@id) -->
     <!-- 	| stmt:str(obta:form, @form) -->
     <!-- 	); -->
-	
+    
     <!-- 	documents.sections.layer[@concept-id].( -->
     <!-- 	  stmt:res(rdf:type, OBT^str:after:':'(@concept-id)) -->
     <!-- 	| stmt:res(obta:document, pmid^section.document.@id) -->
@@ -925,12 +940,12 @@
     <!-- </rdf> -->
 
     <!--
-    <module id="document-richness" class="TabularExport">
-      <outDir>corpora/&corpus;/batch/&batch;</outDir>
-      <files>$</files>
-      <fileName>"document-richness.txt"</fileName>
-      <lines>documents[sections[layer:microorganism and layer:habitats]]</lines>
-      <columns separator=";">
+	<module id="document-richness" class="TabularExport">
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"document-richness.txt"</fileName>
+	<lines>documents[sections[layer:microorganism and layer:habitats]]</lines>
+	<columns separator=";">
 	"&batch;";
 	@id;
 	int(sections.layer:microorganism);
@@ -941,117 +956,117 @@
 	int(sort:nsval(sections.layer:words[@mbto-word], @mbto-word));
 	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @taxid);
 	str:join:'\t'(sort:nsval(sections.layer:habitats, @concept-id), @concept-id);
- 	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @canonical-name);
+	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @canonical-name);
 	str:join:'\t'(sort:nsval(sections.layer:habitats, @concept-id), @concept-name);
 	str:join:'\t'(sort:nsval(sections.layer:words[@mbto-word], @mbto-word), @mbto-word)
-     </columns>
-    </module>
+	</columns>
+	</module>
     -->
 
     <dependencies>
       <index-words class="Action">
-  	<target>documents.sections.layer:sentences[@name != "author"]</target>
-  	<action>id:enumerate:word-index(inside:words)</action>
-  	<setFeatures/>
+	<target>documents.sections.layer:sentences[@name != "author"]</target>
+	<action>id:enumerate:word-index(inside:words)</action>
+	<setFeatures/>
       </index-words>
 
       <index-sentences class="Action">
-  	<target>documents.sections[@name != "author"]</target>
-  	<action>id:enumerate:sentence-index(layer:sentences)</action>
-  	<setFeatures/>
+	<target>documents.sections[@name != "author"]</target>
+	<action>id:enumerate:sentence-index(layer:sentences)</action>
+	<setFeatures/>
       </index-sentences>
 
       <sentences class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"sentences.txt"</fileName>
-  	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
-  	<columns separator=";">
-  	  section.document.@id;
-  	  section.@name;
-  	  @sentence-index;
-  	  start ^ "-" ^ end;
-  	  str:replace(@form, "\n", " ")
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "SENTENCE",
-  	  "OFFSET",
-  	  "FORM"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"sentences.txt"</fileName>
+	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
+	<columns separator=";">
+	  section.document.@id;
+	  section.@name;
+	  @sentence-index;
+	  start ^ "-" ^ end;
+	  str:replace(@form, "\n", " ")
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "SENTENCE",
+	  "OFFSET",
+	  "FORM"
+	</headers>
       </sentences>
 
       <anaphora class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"anaphora.txt"</fileName>
-  	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
-  	<columns separator=";">
-  	  relation.section.document.@id;
-  	  relation.section.@name;
-  	  args:Anaphora.start;
-  	  args:Anaphora.outside:sentences.@sentence-index;
-  	  args:Anaphora.@form;
-  	  args:Ante.start;
-  	  args:Ante.outside:sentences.@sentence-index;
-  	  args:Ante.@form;
-  	  args:AnteTwo.start;
-  	  args:AnteTwo.outside:sentences.@sentence-index;
-  	  args:AnteTwo.@form
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "ANAPHOR OFFSET",
-  	  "ANAPHOR SENTENCE",
-  	  "ANAPHOR FORM",
-  	  "ANTE OFFSET",
-  	  "ANTE SENTENCE",
-  	  "ANTE FORM",
-  	  "ANTE 2 OFFSET",
-  	  "ANTE 2 SENTENCE",
-  	  "ANTE 2 FORM"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"anaphora.txt"</fileName>
+	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
+	<columns separator=";">
+	  relation.section.document.@id;
+	  relation.section.@name;
+	  args:Anaphora.start;
+	  args:Anaphora.outside:sentences.@sentence-index;
+	  args:Anaphora.@form;
+	  args:Ante.start;
+	  args:Ante.outside:sentences.@sentence-index;
+	  args:Ante.@form;
+	  args:AnteTwo.start;
+	  args:AnteTwo.outside:sentences.@sentence-index;
+	  args:AnteTwo.@form
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "ANAPHOR OFFSET",
+	  "ANAPHOR SENTENCE",
+	  "ANAPHOR FORM",
+	  "ANTE OFFSET",
+	  "ANTE SENTENCE",
+	  "ANTE FORM",
+	  "ANTE 2 OFFSET",
+	  "ANTE 2 SENTENCE",
+	  "ANTE 2 FORM"
+	</headers>
       </anaphora>
 
       <dependencies class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"dependencies.txt"</fileName>
-  	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
-  	<columns separator=";">
-  	  relation.section.document.@id;
-  	  relation.section.@name;
-  	  args:sentence.@sentence-index;
-  	  @label;
-  	  args:head.@word-index;
-  	  args:head.@form;
-  	  args:head.@lemma;
-  	  args:head.@pos;
-  	  args:head.start ^ "-" ^ args:head.end;
-  	  args:dependent.@word-index;
-  	  args:dependent.@form;
-  	  args:dependent.@lemma;
-  	  args:dependent.@pos;
-  	  args:dependent.start ^ "-" ^ args:dependent.end
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "SENTENCE",
-  	  "LABEL",
-  	  "HEAD INDEX",
-  	  "HEAD FORM",
-  	  "HEAD LEMMA",
-  	  "HEAD POS",
-  	  "HEAD OFFSET",
-  	  "DEPENDENT INDEX",
-  	  "DEPENDENT FORM",
-  	  "DEPENDENT LEMMA",
-  	  "DEPENDENT POS",
-  	  "DEPENDENT OFFSET"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"dependencies.txt"</fileName>
+	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
+	<columns separator=";">
+	  relation.section.document.@id;
+	  relation.section.@name;
+	  args:sentence.@sentence-index;
+	  @label;
+	  args:head.@word-index;
+	  args:head.@form;
+	  args:head.@lemma;
+	  args:head.@pos;
+	  args:head.start ^ "-" ^ args:head.end;
+	  args:dependent.@word-index;
+	  args:dependent.@form;
+	  args:dependent.@lemma;
+	  args:dependent.@pos;
+	  args:dependent.start ^ "-" ^ args:dependent.end
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "SENTENCE",
+	  "LABEL",
+	  "HEAD INDEX",
+	  "HEAD FORM",
+	  "HEAD LEMMA",
+	  "HEAD POS",
+	  "HEAD OFFSET",
+	  "DEPENDENT INDEX",
+	  "DEPENDENT FORM",
+	  "DEPENDENT LEMMA",
+	  "DEPENDENT POS",
+	  "DEPENDENT OFFSET"
+	</headers>
       </dependencies>
     </dependencies>
   </output>
@@ -1088,7 +1103,7 @@
   <!-- 	  <deleteElements/> -->
   <!-- 	</module> -->
   <!--     </sequence> -->
-      
+  
   <!--     <module id="common" class="Action"> -->
   <!-- 	<target>documents.sections.layer:Species[span:microorganism]</target> -->
   <!-- 	<action>remove:Species|span:microorganism.set:feat:source("Common")</action> -->
@@ -1192,30 +1207,30 @@
   <!-- 	    </args> -->
   <!-- 	  </relation> -->
 
-	  <!--
-	  <text>
-	    <type>"Anaphor"</type>
-	    <instances>layer:mono-anaphora|layer:bi-anaphora</instances>
-	  </text>
-
-	  <relation>
-	    <type>"Coreference"</type>
-	    <instances>relations:coreferences.tuples[args:Ante[@bacteria == "true"]]</instances>
-	    <args>
-	      <Anaphor>args:Anaphora</Anaphor>
-	      <Antecedent>args:Ante</Antecedent>
-	    </args>
-	  </relation>
-
-	  <relation>
-	    <type>"Coreference"</type>
-	    <instances>relations:coreferences.tuples[args:AnteTwo[@bacteria == "true"]]</instances>
-	    <args>
-	      <Anaphor>args:Anaphora</Anaphor>
-	      <Antecedent>args:AnteTwo</Antecedent>
-	    </args>
-	  </relation>
-	  -->
+  <!--
+      <text>
+      <type>"Anaphor"</type>
+      <instances>layer:mono-anaphora|layer:bi-anaphora</instances>
+      </text>
+
+<relation>
+<type>"Coreference"</type>
+<instances>relations:coreferences.tuples[args:Ante[@bacteria == "true"]]</instances>
+<args>
+<Anaphor>args:Anaphora</Anaphor>
+<Antecedent>args:Ante</Antecedent>
+</args>
+</relation>
+
+<relation>
+<type>"Coreference"</type>
+<instances>relations:coreferences.tuples[args:AnteTwo[@bacteria == "true"]]</instances>
+<args>
+<Anaphor>args:Anaphora</Anaphor>
+<Antecedent>args:AnteTwo</Antecedent>
+</args>
+</relation>
+  -->
   <!-- 	</element> -->
   <!--     </annotationSets> -->
   <!--   </module> -->
@@ -1237,19 +1252,19 @@
     <index class="AlvisDBIndexer">
       <indexDir>corpora/&corpus;/batch/&batch;/adb</indexDir>
       <elements>
-  	<relations>
-  	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
-  	  <id>"&batch;_" ^ id:unique</id>
-  	  <name>"Localization"</name>
-  	  <type>"localization"</type>
-  	  <args>args:Bacterium|args:Localization</args>
-  	  <arg-id>if @taxid then @taxid else @concept-id</arg-id>
-  	  <arg-name>if @taxid then @canonical-name else @concept-name</arg-name>
-  	  <ancestors>nav:features:ancestors</ancestors>
-  	  <ancestor-id>@value</ancestor-id>
-  	  <arg-doc>section.document.@id</arg-doc>
-  	  <arg-sec>section.@name</arg-sec>
-  	</relations>
+	<relations>
+	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
+	  <id>"&batch;_" ^ id:unique</id>
+	  <name>"Localization"</name>
+	  <type>"localization"</type>
+	  <args>args:Bacterium|args:Localization</args>
+	  <arg-id>if @taxid then @taxid else @concept-id</arg-id>
+	  <arg-name>if @taxid then @canonical-name else @concept-name</arg-name>
+	  <ancestors>nav:features:ancestors</ancestors>
+	  <ancestor-id>@value</ancestor-id>
+	  <arg-doc>section.document.@id</arg-doc>
+	  <arg-sec>section.@name</arg-sec>
+	</relations>
       </elements>
     </index>
   </adb>
@@ -1266,19 +1281,19 @@
     <propertyKeys/>
     <documents>
       <fields>
-  	<instances>sections:title | sections:abstract</instances>
-  	<annotations>
-  	  <instances>layer:microorganism</instances>
-  	  <text>"{taxon}" ^ @path ^ "/"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:sentences</instances>
-  	  <text>"{SENT}"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:habitats</instances>
-  	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
-  	</annotations>
+	<instances>sections:title | sections:abstract</instances>
+	<annotations>
+	  <instances>layer:microorganism</instances>
+	  <text>"{taxon}" ^ @path ^ "/"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:sentences</instances>
+	  <text>"{SENT}"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:habitats</instances>
+	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
+	</annotations>
 	<annotations>
 	  <instances>layer:phenotypes</instances>
 	  <text>"{phenotype}" ^ @concept-path ^ "/"</text>
@@ -1287,112 +1302,112 @@
 	  <instances>layer:uses</instances>
 	  <text>"{use}" ^ @concept-path ^ "/"</text>
 	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
 
 	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
 
       </fields>
       <fields>
-  	<instances>nav:features:mesh-name</instances>
-  	<field-name>"mesh"</field-name>
-  	<keyword>@value</keyword>
+	<instances>nav:features:mesh-name</instances>
+	<field-name>"mesh"</field-name>
+	<keyword>@value</keyword>
       </fields>
       <fields>
-  	<instances>sections:author</instances>
+	<instances>sections:author</instances>
       </fields>
       <fields>
-  	<instances>sections:author</instances>
-  	<field-name>"full-author"</field-name>
-  	<keyword>contents</keyword>
+	<instances>sections:author</instances>
+	<field-name>"full-author"</field-name>
+	<keyword>contents</keyword>
       </fields>
       <fields>
-  	<instances>$</instances>
-  	<field-name>"pmid"</field-name>
-  	<keyword>@id</keyword>
+	<instances>$</instances>
+	<field-name>"pmid"</field-name>
+	<keyword>@id</keyword>
       </fields>
       <fields>
-  	<instances>$[@year]</instances>
-  	<field-name>"year"</field-name>
-  	<keyword>@year</keyword>
+	<instances>$[@year]</instances>
+	<field-name>"year"</field-name>
+	<keyword>@year</keyword>
       </fields>
       <fields>
-  	<instances>$[@journal]</instances>
-  	<field-name>"journal"</field-name>
-  	<keyword>@journal</keyword>
+	<instances>$[@journal]</instances>
+	<field-name>"journal"</field-name>
+	<keyword>@journal</keyword>
       </fields>
       <fields>
-        <instances>$[@url]</instances>
-        <field-name>"url"</field-name>
-        <keyword>document.@url</keyword>
+	<instances>$[@url]</instances>
+	<field-name>"url"</field-name>
+	<keyword>document.@url</keyword>
       </fields>
     </documents>
   </index>
 
- <index-food class="AlvisIRIndexer">
+  <index-food class="AlvisIRIndexer">
     <indexDir>corpora/&corpus;/batch/&batch;/index-food</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
@@ -1404,19 +1419,19 @@
     <propertyKeys/>
     <documents>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="title"] | sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="abstract"]</instances>
-  	<annotations>
-  	  <instances>layer:microorganism</instances>
-  	  <text>"{taxon}" ^ @path ^ "/"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:sentences</instances>
-  	  <text>"{SENT}"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:habitats</instances>
-  	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
-  	</annotations>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="title"] | sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="abstract"]</instances>
+	<annotations>
+	  <instances>layer:microorganism</instances>
+	  <text>"{taxon}" ^ @path ^ "/"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:sentences</instances>
+	  <text>"{SENT}"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:habitats</instances>
+	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
+	</annotations>
 	<annotations>
 	  <instances>layer:phenotypes</instances>
 	  <text>"{phenotype}" ^ @concept-path ^ "/"</text>
@@ -1425,148 +1440,236 @@
 	  <instances>layer:uses</instances>
 	  <text>"{use}" ^ @concept-path ^ "/"</text>
 	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
 	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
       </fields>
       <fields>
-  	<instances>nav:features:mesh-name</instances>
-  	<field-name>"mesh"</field-name>
-  	<keyword>@value</keyword>
+	<instances>nav:features:mesh-name</instances>
+	<field-name>"mesh"</field-name>
+	<keyword>@value</keyword>
       </fields>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
       </fields>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
-  	<field-name>"full-author"</field-name>
-  	<keyword>contents</keyword>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
+	<field-name>"full-author"</field-name>
+	<keyword>contents</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt"]</instances>
-  	<field-name>"pmid"</field-name>
-  	<keyword>@id</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt"]</instances>
+	<field-name>"pmid"</field-name>
+	<keyword>@id</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @year]</instances>
-  	<field-name>"year"</field-name>
-  	<keyword>@year</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @year]</instances>
+	<field-name>"year"</field-name>
+	<keyword>@year</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @journal]</instances>
-  	<field-name>"journal"</field-name>
-  	<keyword>@journal</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @journal]</instances>
+	<field-name>"journal"</field-name>
+	<keyword>@journal</keyword>
       </fields>
       <fields>
-        <instances>$[@url]</instances>
-        <field-name>"url"</field-name>
-        <keyword>document.@url</keyword>
+	<instances>$[@url]</instances>
+	<field-name>"url"</field-name>
+	<keyword>document.@url</keyword>
       </fields>
     </documents>
   </index-food>
 
-<!-- HTML visualization -->
-<add-feature class="Action">
-  <target>documents.sections.layer:habitats</target>
-  <action>set:feat:ne-type("Habitat")</action>
-  <setFeatures/>
-</add-feature>
-<!-- <module id="add-feature0" class="Action"> -->
-<!--   <target>documents.sections.layer:habitats</target> -->
-<!--   <action>set:feat:before(target.overlapping:words{0}.@form)</action> -->
-<!--   <setFeatures/> -->
-<!-- </module> -->
-<add-feature2 class="Action">
-  <target>documents.sections.layer:phenotypes</target>
-  <action>set:feat:ne-type("Phenotype")</action>
-  <setFeatures/>
-</add-feature2>
-<add-feature3 class="Action">
-  <target>documents.sections.layer:microorganism</target>
-  <action>set:feat:ne-type("Microorganism")</action>
-  <setFeatures/>
-</add-feature3>
-<html class="QuickHTML">
-  <active>false</active>
-  <outDir>corpora/&corpus;/batch/&batch;/html</outDir>
-  <classFeature>ne-type</classFeature>
-  <layers>phenotypes,microorganism,habitats</layers>
-  <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
-</html>
-
-<words class="TabularExport">
-  <outDir>corpora/&corpus;/batch/&batch;</outDir>
-  <files>$</files>
-  <fileName>"words.txt"</fileName>
-  <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
-  <columns separator=";">
-    section.document.@id;
-    @form
-  </columns>
-</words>
+  <!-- HTML visualization -->
+  <add-feature class="Action">
+    <target>documents.sections.layer:habitats</target>
+    <action>set:feat:ne-type("Habitat")</action>
+    <setFeatures/>
+  </add-feature>
+  <!-- <module id="add-feature0" class="Action"> -->
+  <!--   <target>documents.sections.layer:habitats</target> -->
+  <!--   <action>set:feat:before(target.overlapping:words{0}.@form)</action> -->
+  <!--   <setFeatures/> -->
+  <!-- </module> -->
+  <add-feature2 class="Action">
+    <target>documents.sections.layer:phenotypes</target>
+    <action>set:feat:ne-type("Phenotype")</action>
+    <setFeatures/>
+  </add-feature2>
+  <add-feature3 class="Action">
+    <target>documents.sections.layer:microorganism</target>
+    <action>set:feat:ne-type("Microorganism")</action>
+    <setFeatures/>
+  </add-feature3>
+  <html class="QuickHTML">
+    <active>false</active>
+    <outDir>corpora/&corpus;/batch/&batch;/html</outDir>
+    <classFeature>ne-type</classFeature>
+    <layers>phenotypes,microorganism,habitats</layers>
+    <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
+  </html>
+
+  <words class="TabularExport">
+    <outDir>corpora/&corpus;/batch/&batch;</outDir>
+    <files>$</files>
+    <fileName>"words.txt"</fileName>
+    <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
+    <columns separator=";">
+      section.document.@id;
+      @form
+    </columns>
+  </words>
+
+  <bionlp-st-a2>
+    <habitats class="TabularExport">
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:habitats</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Habitat " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </habitats>
+    
+    <phenotypes class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:phenotypes</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Phenotype " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </phenotypes>
+    
+    <microorganisms class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:microorganism</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Microorganism " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </microorganisms>
+
+    <obt class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:habitats|layer:phenotypes</lines>
+      <columns separator=";">
+	"N" ^ id:unique;
+	"OntoBiotope Annotation:T" ^ id:unique ^ " Referent:" ^ @concept-id
+      </columns>
+    </obt>
+
+    <taxid class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:microorganism</lines>
+      <columns separator=";">
+	"N" ^ id:unique;
+	"NCBI_Taxonomy Annotation:T" ^ id:unique ^ " Referent:" ^ str:replace(@taxid, "ncbi:", "")
+      </columns>
+    </taxid>
+
+    <lives-in class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>relations:CooccurrenceLocalization.tuples[args:Localization.@concept-id != ""]</lines>
+      <columns separator=";">
+	"R" ^ id:unique;
+	"Lives_In Microorganism:T" ^ args:Bacterium.id:unique ^ " Location:T" ^ args:Localization.id:unique
+      </columns>
+    </lives-in>
+
+    <exhibits class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>relations:PhenotypeRelation.tuples</lines>
+      <columns separator=";">
+	"R" ^ id:unique;
+	"Exhibits Microorganism:T" ^ args:Microorganism.id:unique ^ " Property:T" ^ args:Phenotype.id:unique
+      </columns>
+    </exhibits>
+  </bionlp-st-a2>
 
 
   <success class="TabularExport">
diff --git a/process-evaluate_BioNLP-OST.snakefile b/process-evaluate_BioNLP-OST.snakefile
new file mode 100644
index 00000000..e9f494ff
--- /dev/null
+++ b/process-evaluate_BioNLP-OST.snakefile
@@ -0,0 +1,86 @@
+## local rule
+# localrules: all, concat_results
+
+## config file
+configfile: "config/config.yaml"
+
+## document batches
+BATCHES, = glob_wildcards(config["BIONLPOST_BATCHES_HOME"] + "/{id}/bionlp-st")
+
+
+'''
+all
+'''
+rule all:
+	input:
+		log=expand("corpora/BioNLP-OST-2019/batch/{B}/eval.json", B=BATCHES),
+                scores=expand("corpora/BioNLP-OST-2019/batch/{B}/eval.json", B=BATCHES)
+
+
+'''
+Extract entities in different corpus 
+batches using the alvisnlp plan (entities.plan)
+'''
+rule run_bionlp_prediction:
+	input:
+		dir=directory("corpora/BioNLP-OST-2019/batch/{B}/bionlp-st"),
+		xslt="corpora/microbes-2019/microbes-2019-pubmed2alvisnlp.xslt"
+	output:
+		relations="corpora/BioNLP-OST-2019/batch/{B}/relations.txt",
+		phenotypeRelations="corpora/BioNLP-OST-2019/batch/{B}/phenotype-relations.txt",
+		usesRelations="corpora/BioNLP-OST-2019/batch/{B}/uses-relations.txt",
+		microorganisms="corpora/BioNLP-OST-2019/batch/{B}/microorganisms.txt",
+		habitats="corpora/BioNLP-OST-2019/batch/{B}/habitats.txt",
+		phenotypes="corpora/BioNLP-OST-2019/batch/{B}/phenotypes.txt",
+		uses="corpora/BioNLP-OST-2019/batch/{B}/uses.txt",
+		index=directory("corpora/BioNLP-OST-2019/batch/{B}/index"),
+		a2=directory("corpora/BioNLP-OST-2019/batch/{B}/a2")
+	log:"corpora/BioNLP-OST-2019/batch/{B}/alvisnlp.log"
+	params:
+		batch="{B}",
+		corpus='BioNLP-OST-2019',
+                inhibitSyntax='inhibit-syntax',
+		onto='ancillaries/BioNLP-OST+EnovFood',
+                ontobiotopeUse='ancillaries/Use_V2',
+		plan='plans/entities.plan',
+		dir='corpora/BioNLP-OST-2019/batch/{B}/',
+		taxid_microorganisms='ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt',
+                taxa_id_full='ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt'
+	singularity:config["SINGULARITY_IMG"]
+	shell:"""
+		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
+		-log {log} \
+		-alias format bionlp-st \
+		-alias input-dir {input.dir} \
+		-alias input-xslt {input.xslt} \
+		-alias outputDir {params.dir} \
+		-environmentEntities \
+		-entity corpus {params.corpus} \
+		-feat inhibit-syntax {params.inhibitSyntax} \
+		-entity ontobiotope {params.onto} \
+		-entity ontobiotope-use {params.ontobiotopeUse} \
+		-entity batch {params.batch} \
+		-alias taxid_microorganisms {params.taxid_microorganisms} \
+		-alias taxa+id_full {params.taxa_id_full} \
+		{params.plan}	    
+	      """
+
+rule archive_prediction:
+    input:
+        a2=directory("corpora/BioNLP-OST-2019/batch/{B}/a2")
+    output:
+        zip="corpora/BioNLP-OST-2019/batch/{B}/predictions.zip"
+    shell:
+        """zip -9 {output.zip} {input.a2}/*.a2"""
+
+        
+rule evaluate:
+    input:
+        zip="corpora/BioNLP-OST-2019/batch/{B}/predictions.zip"
+    output:
+        scores="corpora/BioNLP-OST-2019/batch/{B}/eval.json"
+    params:
+        api=config["BIONLPOST_API"],
+        task="{B}"
+    shell:
+        """curl -o {output.scores} -X POST "{params.api}/task/{params.task}/test/evaluate" -H "accept: application/json" -H "Content-Type: multipart/form-data" -F "resamples=0" -F "detailed=false" -F "alternate=true" -F "zipfile=@{input.zip};type=application/zip" """
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 9ae857aa..9cda4f24 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -57,6 +57,7 @@ rule run_pubmed_entities:
 	shell:"""
 		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
 		-log {log} \
+		-alias format pubmed \
 		-alias input {input.file} \
 		-alias input-xslt {input.xslt} \
 		-alias outputDir {params.dir} \
-- 
GitLab


From c24430eef20aa54ed3c013e238f408fa41c017bb Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:08:50 +0100
Subject: [PATCH 02/64] documented BioNLP-OST evaluation

---
 README.md                    |  3 ++
 docs/7-process-bionlp-ost.md | 75 ++++++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 docs/7-process-bionlp-ost.md

diff --git a/README.md b/README.md
index 6c211ffd..a44c5812 100644
--- a/README.md
+++ b/README.md
@@ -31,6 +31,9 @@ We use [Snakemake](https://snakemake.readthedocs.io) pipelines to materialize th
 6. **`Process PubMed corpus`** to extract microorganisms, habitats of texts from Pubmed. 
 [details here...](docs/6-process-pubmed-data.md)
 
+7. **`Process BioNLP-OST 2019 test corpus`** to evaluate the results on a reference dataset. 
+[details here...](docs/7-process-bionlp-ost.md)
+
 
 The workflow relies on the following `structure of folders` to manage the resources:
 ```
diff --git a/docs/7-process-bionlp-ost.md b/docs/7-process-bionlp-ost.md
new file mode 100644
index 00000000..f2736d4a
--- /dev/null
+++ b/docs/7-process-bionlp-ost.md
@@ -0,0 +1,75 @@
+## About
+This pipeline is the same as the PubMed processing one, using the same alvisnlp plan `plans/entities.plan`.
+Rather than processing PubMed abstracts, it processes the test data from three tasks of the [BioNLP-OST 2019 Bacteria Biotope](https://sites.google.com/view/bb-2019/home), then evaluates the prediction with the API of the dedicated [online evaluation tool](http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/index.html).
+
+The three tasks are:
+* `BB-norm+ner`: evaluates NER and normalization (Microorganism, Habitat and Phenotype).
+* `BB-rel+ner`: evaluates NER and relation extraction (Lives_In and Exhibits).
+* `BB-kb+ner`: evaluates knowledge base extraction performance.
+
+The three datasets are available in `corpora/BioNLP-OST-2019/batch`. 
+
+## Run the pipeline
+
+```
+snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 30 --jobs 3 \
+--snakefile process-evaluate_BioNLP-OST.snakefile \
+--cluster "qsub -v PYTHONPATH=''  -V -cwd -e log/ -o log/ -q short.q -pe thread 2" \
+--restart-times 4 all
+```
+## Display the DAG
+
+```
+snakemake --verbose \
+--dag \
+--printshellcmds \
+--use-singularity \
+--forceall \
+--nolock \
+--dry-run \
+--reason \
+--cores 4  \
+--snakefile  process-evaluate_BioNLP-OST.snakefile \
+all
+| dot -Tsvg >  process-evaluate_BioNLP-OST.snakefile.svg
+
+show  process-evaluate_BioNLP-OST.snakefile.svg
+```
+
+## **Resources used**
+
+The pipeline relies on the following alvisnlp plan:
+* `entities.plan`
+	* `taxa.plan`
+		* `strains-1.plan`
+	* `syntax.plan`
+		* `segmentation.plan`
+			* `number-and-dates.plan`
+	* `strains-2.plan`
+	* `pos-tag-lemma-postprocessing.plan`
+	* `tomap-habitats.plan`
+		* `tag-food-derivative.plan`
+		* `tag-food-process.plan`
+	* `tomap-microbial-phenotypes.plan`
+	* `use-extraction.plan`
+	* `anaphora.plan`
+
+The pipeline handles the following resources :
+* inputs
+    * `corpora/BioNLP-OST-2019/*/bionlp-st`
+    * `ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+    * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo`
+    * `ancillaries/Use_V2.obo`
+* outputs
+	* `corpora/BioNLP-OST-2019/batch/*/eval.json`
+* programs
+    * `alvisnlp singularity container`
+    * `python env`
+
+
+|solution |nb steps |
+|--------|--------|
+|AlvisNLP plans | xxx |
+|bash scripts| xxx |
+|python scripts | xxx |
+| java jars | xxx |
-- 
GitLab


From 573dbf4e6a6277ddd3a649c32b9bccc01e0751f8 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:17:09 +0100
Subject: [PATCH 03/64] ignore more output files

---
 .gitignore | 51 +++++++++++++++++++++++++++------------------------
 1 file changed, 27 insertions(+), 24 deletions(-)

diff --git a/.gitignore b/.gitignore
index 09e7e901..633dc797 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,30 +19,33 @@ corpora/genbank/mapped_habitats.txt
 corpora/genbank/mapped_taxids.txt
 corpora/genbank/taxids.txt
 corpora/genbank/test-3.2.txt
-corpora/microbes-2019/batch/*/adb/
-corpora/microbes-2019/batch/*/alvisnlp.log
-corpora/microbes-2019/batch/*/anaphora.txt
-corpora/microbes-2019/batch/*/bacteria.txt
-corpora/microbes-2019/batch/*/dependencies.txt
-corpora/microbes-2019/batch/*/doc-mesh.txt
-corpora/microbes-2019/batch/*/geo.txt
-corpora/microbes-2019/batch/*/habitats.txt
-corpora/microbes-2019/batch/*/index-food/
-corpora/microbes-2019/batch/*/index/
-corpora/microbes-2019/batch/*/microorganisms-short.txt
-corpora/microbes-2019/batch/*/microorganisms.txt
-corpora/microbes-2019/batch/*/phenotype-relations.txt
-corpora/microbes-2019/batch/*/phenotypes.txt
-corpora/microbes-2019/batch/*/relations.txt
-corpora/microbes-2019/batch/*/sentences.txt
-corpora/microbes-2019/batch/*/success.txt
-corpora/microbes-2019/batch/*/taxa.txt
-corpora/microbes-2019/batch/*/uses-relations.txt
-corpora/microbes-2019/batch/*/uses.txt
-corpora/microbes-2019/batch/*/words.txt
-corpora/microbes-2019/batch/*/yatea-var/
-corpora/microbes-2019/batch/*/yatea/
-corpora/microbes-2019/expander/
+corpora/*-2019/batch/*/adb/
+corpora/*-2019/batch/*/alvisnlp.log
+corpora/*-2019/batch/*/anaphora.txt
+corpora/*-2019/batch/*/bacteria.txt
+corpora/*-2019/batch/*/dependencies.txt
+corpora/*-2019/batch/*/doc-mesh.txt
+corpora/*-2019/batch/*/geo.txt
+corpora/*-2019/batch/*/habitats.txt
+corpora/*-2019/batch/*/index-food/
+corpora/*-2019/batch/*/index/
+corpora/*-2019/batch/*/microorganisms-short.txt
+corpora/*-2019/batch/*/microorganisms.txt
+corpora/*-2019/batch/*/phenotype-relations.txt
+corpora/*-2019/batch/*/phenotypes.txt
+corpora/*-2019/batch/*/relations.txt
+corpora/*-2019/batch/*/sentences.txt
+corpora/*-2019/batch/*/success.txt
+corpora/*-2019/batch/*/taxa.txt
+corpora/*-2019/batch/*/uses-relations.txt
+corpora/*-2019/batch/*/uses.txt
+corpora/*-2019/batch/*/words.txt
+corpora/*-2019/batch/*/yatea-var/
+corpora/*-2019/batch/*/yatea/
+corpora/*-2019/expander/
+corpora/*-2019/batch/*/a2/
+corpora/BioNLP-OST-2019/batch/*/eval.json
+corpora/BioNLP-OST-2019/batch/*/predictions.zip
 corpora/microbes-2019/*.full.txt
 corpora/microbes-2019/index/
 .snakemake/
-- 
GitLab


From 13cba003396bc22a27111d31ede398af10bb1596 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:20:51 +0100
Subject: [PATCH 04/64] ignore some softwares

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 633dc797..e2b67045 100644
--- a/.gitignore
+++ b/.gitignore
@@ -64,3 +64,6 @@ ancillaries/yatea-ncbi/
 ancillaries/yatea-var/
 ancillaries/yatea/
 yatea-train/
+softwares/alvisir-install/
+softwares/*.sif
+softwares/obo-utils
-- 
GitLab


From b97ca8ed790c06f7665313cf4901685b00da607b Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 14:00:40 +0100
Subject: [PATCH 05/64] create dummy bionlp-st directory

---
 process_PubMed_corpus.snakefile | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 9cda4f24..b5a20ac3 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -23,7 +23,14 @@ rule all:
 		florilege_Habitat_result="corpora/florilege/pubmed/PubMed-Habitat.txt",
 		florilege_Phenotype_result="corpora/florilege/pubmed/PubMed-Phenotype.txt",
 		florilege_Use_result="corpora/florilege/pubmed/PubMed-Use.txt"
-		
+
+
+rule create_dummy_bionlp_st_dir:
+    output:
+        dummy=directory("corpora/microbes-2019/batch/{B}/bionlp-st")
+    shell:
+        '''mkdir -p {output.dummy}'''
+
 
 '''
 Extract entities in different corpus 
@@ -32,6 +39,7 @@ batches using the alvisnlp plan (entities.plan)
 rule run_pubmed_entities:
 	input:
 		file="corpora/microbes-2019/batch/{B}/batch.xml",
+		dummy=("corpora/microbes-2019/batch/{B}/bionlp-st"),
 		xslt="corpora/microbes-2019/microbes-2019-pubmed2alvisnlp.xslt"
 	output:
 		relations="corpora/microbes-2019/batch/{B}/relations.txt",
@@ -54,7 +62,8 @@ rule run_pubmed_entities:
 		taxid_microorganisms='ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt',
                 taxa_id_full='ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt'
 	singularity:config["SINGULARITY_IMG"]
-	shell:"""
+	shell:
+            """
 		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
 		-log {log} \
 		-alias format pubmed \
-- 
GitLab


From 7509873a80bad048786cab7ca93225133809f411 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:04:20 +0100
Subject: [PATCH 06/64] Add new file

---
 corpora%2Fflorilege/labels.stats | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 corpora%2Fflorilege/labels.stats

diff --git a/corpora%2Fflorilege/labels.stats b/corpora%2Fflorilege/labels.stats
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/corpora%2Fflorilege/labels.stats
@@ -0,0 +1 @@
+
-- 
GitLab


From cbb578e972a7e89c74df9c9c7eaeac520a7fd924 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:05:03 +0100
Subject: [PATCH 07/64] Update labels.stats

---
 {corpora%2Fflorilege => corpora/florilege}/labels.stats | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {corpora%2Fflorilege => corpora/florilege}/labels.stats (100%)

diff --git a/corpora%2Fflorilege/labels.stats b/corpora/florilege/labels.stats
similarity index 100%
rename from corpora%2Fflorilege/labels.stats
rename to corpora/florilege/labels.stats
-- 
GitLab


From 8fc3aee79abe598d417fcdfa57baeaffa74dfbca Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:44:50 +0100
Subject: [PATCH 08/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 8b137891..7bd7b0cb 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1 +1,24 @@
+id,label,file
+cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
+cirm_002,nombre d'entrées cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
+cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_taxids.txt
+cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
+cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
+cirm_006,nombre d'habitat de cirm-Levure,cirm/mapped_yeast_habitats.txt
+genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
+genbank_002,nombre de taxon de genbank,genbank/mapped_taxids.txt
+genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
+dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
+dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
+dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
+pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
+pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
+pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
+pubmed_004,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
+pubmed_005,nombre de relations du type #Phenotype-Relations pubmed,microbes-2019/phenotype-relations.txt
+pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
+pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
+pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
+pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
+
 
-- 
GitLab


From cb3e1fa7ca65061b0a25cdd1e970f6db3e7d7d60 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 15:42:33 +0100
Subject: [PATCH 09/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 7bd7b0cb..7ca2a12a 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -20,5 +20,14 @@ pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotyp
 pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
 pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
-
-
+eval_001, corpus utilisés, BioNLP-OST-2019
+eval_002, date, None
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-- 
GitLab


From d6f227ce373d30d67d24ec0a1a7515c9899f468b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 10:21:46 +0100
Subject: [PATCH 10/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 7ca2a12a..fe279abc 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -26,8 +26,8 @@ eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-201
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
 eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
 eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-norm+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-- 
GitLab


From 909409fa308ac0fb3e6f333e57c24689a3ac8903 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:03:30 +0100
Subject: [PATCH 11/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 32 ++++++++++++++++++++++++++------
 1 file changed, 26 insertions(+), 6 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9ce6bc95..e107cfdb 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -11,16 +11,35 @@ rule all:
 SOURCES=["cirm", "genbank", "dsmz", "microbes-2019"]
 
 '''
-cirm | nb entrees | count_lines(corpora/cirm/2019-07-05/extraction_3-fv.csv)
-cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2017/data_CIRM_levures_extraction_09032017.csv)
+cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx)
+cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
+'''
+ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
+rule count_lines_cirm:
+	input:
+		file="corpora/cirm/{file}"
+	output:
+		stats="corpora/cirm/stats/{file}_stats.csv"
+	params:
+		result="cirm/{file}",
+		c0="source",
+		v0="cirm",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+'''
 cirm | nb entites | count_lines(corpora/cirm/mapped_taxids.txt)
-cirm | nb yeast entities | count_lines(corpora/cirm/yeast_taxa.txt)
+cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-ENTREES_CIRM = ["2019-07-05/extraction_3-fv.csv", "Levures_2017/data_CIRM_levures_extraction_09032017.csv"]
-SORTIES_CIRM = ["mapped_taxids.txt", "yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
-FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
+SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
 rule count_lines_cirm:
@@ -41,6 +60,7 @@ rule count_lines_cirm:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
 '''
 merge
 '''
-- 
GitLab


From 74f1b7d0eaf531d90968036f17eabfd0841b6f9c Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:06:33 +0100
Subject: [PATCH 12/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index e107cfdb..a3460936 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -76,11 +76,11 @@ rule merge_stats_cirm:
 		result.to_csv(output.result, index=False)
 
 '''
-genbank | nb entrees | count_lines(corpora/genbank/req1_sup800_bacteria-descriptors.csv)
+genbank | nb entrees | count_lines(corpora/genbank/corpora/genbank/GenBank_extraction_20210127.tsv)
 genbank | nb entites | count_lines(corpora/genbank/mapped_taxids.txt)
 genbank | nb habitats | count_lines(corpora/genbank/mapped_habitats.txt)
 '''
-ENTREES_GENBANK = ["req1_sup800_bacteria-descriptors.csv"]
+ENTREES_GENBANK = ["corpora/genbank/GenBank_extraction_20210127.tsv"]
 SORTIES_GENBANK = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_GENBANK = ENTREES_GENBANK + SORTIES_GENBANK
 '''
-- 
GitLab


From cf79c788afa29573935ebf165bd210afdac612df Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:31:03 +0100
Subject: [PATCH 13/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 63 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 58 insertions(+), 5 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index a3460936..b0bdda44 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -15,7 +15,7 @@ cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_
 cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
 '''
 ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
-rule count_lines_cirm:
+rule stats_cirm:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -42,7 +42,7 @@ cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
-rule count_lines_cirm:
+rule stats_cirm:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -85,7 +85,7 @@ SORTIES_GENBANK = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_GENBANK = ENTREES_GENBANK + SORTIES_GENBANK
 '''
 '''
-rule count_lines_genbank:
+rule stats_genbank:
 	input:
 		file="corpora/genbank/{file}"
 	output:
@@ -127,7 +127,7 @@ SORTIES_DSMZ = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_DSMZ = ENTREES_DSMZ + SORTIES_DSMZ
 '''
 '''
-rule count_lines_dsmz:
+rule stats_dsmz:
 	input:
 		file="corpora/dsmz/{file}"
 	output:
@@ -179,7 +179,7 @@ FILES_PUBMED = ENTREES_PUBMED + SORTIES_PUBMED
 '''
 '''
 
-rule count_lines_pubmed:
+rule stats_pubmed:
 	input:
 		file="corpora/microbes-2019/{file}"
 	output:
@@ -212,6 +212,59 @@ rule merge_stats_pubmed:
 		result.to_csv(output.result, index=False)
 
 
+
+'''
+eval_001, corpus utilisés, BioNLP-OST-2019
+eval_002, date, None
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+'''
+ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
+SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
+FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
+
+'''
+'''
+
+rule stats_veal:
+	input:
+		file="corpora/microbes-2019/{file}"
+	output:
+		stats="corpora/microbes-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+'''
+merge
+'''
+rule merge_stats_eval:
+	input:
+		files=expand("corpora/microbes-2019/stats/{file}_stats.csv", file=FILES_PUBMED)
+	output:
+		result="corpora/microbes-2019/stats/stats.full.csv"
+	run:
+		import pandas
+		frames = [ pandas.read_csv(f) for f in input.files ]
+		result = pandas.concat(frames)
+		result.to_csv(output.result, index=False)
+
 '''
 merge all
 '''
-- 
GitLab


From ac35e390453c8a84afe84764ee479d3683dff4fc Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 18:15:15 +0100
Subject: [PATCH 14/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 89 ++++++++++++++++++++++++++++++++++------
 1 file changed, 77 insertions(+), 12 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index b0bdda44..f8e06321 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,3 +1,16 @@
+def get_score_stats(file, entity):
+	import json
+	data = json.load(open(file))
+	for d in (data['evaluation'])['global-evaluations']:
+		for s in d['scorings']:
+			if s['name'] == entity:
+				list = s['measures']
+				list[0]
+
+
+
+
+
 '''
 all
 '''
@@ -216,15 +229,15 @@ rule merge_stats_pubmed:
 '''
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_001
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_002
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_003
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_004
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_001
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_002
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_003
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json#eval_BB19-kb+ner_001#eval_BB19-kb+ner_002
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json#eval_BB19-kb+ner_002
 '''
 ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
 SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
@@ -233,11 +246,62 @@ FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
 '''
 '''
 
-rule stats_veal:
+rule stats_eval_BB19-norm+ner:
 	input:
-		file="corpora/microbes-2019/{file}"
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
 	output:
-		stats="corpora/microbes-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_json(input.file)
+		df1["evaluation"]
+		for d in (data['evaluation'])['global-evaluations']:
+			for s in d['scorings']:
+				if s['name'] == "Habitats":
+					for e in s['measures']:
+						print(e['name'])
+						print(e['value'])
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+
+'''
+'''
+
+rule stats_eval_BB19-rel+ner:
+	input:
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json
+	output:
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+
+'''
+'''
+
+rule stats_eval_BB19-kb+ner:
+	input:
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+	output:
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
 		c0="source",
@@ -251,6 +315,7 @@ rule stats_veal:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+
 '''
 merge
 '''
-- 
GitLab


From 6a5e31bf1e00c01c6e47f8dadc2c01ea3624a3bb Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 20:10:07 +0100
Subject: [PATCH 15/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index f8e06321..09581902 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,11 +1,12 @@
-def get_score_stats(file, entity):
+def get_score_stats(file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", entity="Habitats"):
 	import json
 	data = json.load(open(file))
 	for d in (data['evaluation'])['global-evaluations']:
-		for s in d['scorings']:
+		scorings = d['scorings']
+		for s in scorings:
 			if s['name'] == entity:
-				list = s['measures']
-				list[0]
+				return s['measures'][0]
+	return None
 
 
 
-- 
GitLab


From 02f295c1372bb4b51b4a11c0b754ab65001310e4 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 20:22:57 +0100
Subject: [PATCH 16/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 09581902..5311c9ba 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -261,14 +261,9 @@ rule stats_eval_BB19-norm+ner:
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_json(input.file)
-		df1["evaluation"]
-		for d in (data['evaluation'])['global-evaluations']:
-			for s in d['scorings']:
-				if s['name'] == "Habitats":
-					for e in s['measures']:
-						print(e['name'])
-						print(e['value'])
+		get_score_stats(input.file, "Habitats")
+		get_score_stats(input.file, "Phenotypes")
+		get_score_stats(input.file, "Microorganisms")
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
-- 
GitLab


From 9c6553bfa463d4ee1ac23607142e8f27ba789b1b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:06:30 +0100
Subject: [PATCH 17/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 77 +++++++++++++++++++---------------------
 1 file changed, 36 insertions(+), 41 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 5311c9ba..743c801b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,16 +1,3 @@
-def get_score_stats(file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", entity="Habitats"):
-	import json
-	data = json.load(open(file))
-	for d in (data['evaluation'])['global-evaluations']:
-		scorings = d['scorings']
-		for s in scorings:
-			if s['name'] == entity:
-				return s['measures'][0]
-	return None
-
-
-
-
 
 '''
 all
@@ -22,7 +9,7 @@ rule all:
 
 
 
-SOURCES=["cirm", "genbank", "dsmz", "microbes-2019"]
+SOURCES=["cirm", "genbank", "dsmz", "microbes-2019", "BioNLP-OST-2019"]
 
 '''
 cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx)
@@ -242,84 +229,92 @@ eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/ev
 '''
 ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
 SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
-FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
+FILES_EVAL = ["BB19-norm+ner", "BB19-rel+ner", "BB19-kb+ner"]
+
+def get_score_stats(file, entity):
+	import json
+	data = json.load(open(file))
+	for d in (data['evaluation'])['global-evaluations']:
+		scorings = d['scorings']
+		for s in scorings:
+			if s['name'] == entity:
+				return s['measures'][0]
+	return None
+
 
 '''
 '''
-
 rule stats_eval_BB19-norm+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-norm+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-norm+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		get_score_stats(input.file, "Habitats")
-		get_score_stats(input.file, "Phenotypes")
-		get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		h = get_score_stats(input.file, "Habitats")
+		p = get_score_stats(input.file, "Phenotypes")
+		m = get_score_stats(input.file, "Microorganisms")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
 '''
 '''
-
 rule stats_eval_BB19-rel+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json
+		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-rel+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-rel+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		l = get_score_stats(input.file, "Lives_In")
+		e = get_score_stats(input.file, "Exhibits")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
 '''
 '''
-
 rule stats_eval_BB19-kb+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-kb+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-kb+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		s = get_score_stats(input.file, "Standard scoring")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring"], params.c2: [s['name'], s['value']]})
 		df2.to_csv(output.stats, index=False)
 
-
 '''
 merge
 '''
 rule merge_stats_eval:
 	input:
-		files=expand("corpora/microbes-2019/stats/{file}_stats.csv", file=FILES_PUBMED)
+		files=expand("corpora/BioNLP-OST-2019/stats/{file}_stats.csv", file=FILES_EVAL)
 	output:
-		result="corpora/microbes-2019/stats/stats.full.csv"
+		result="corpora/BioNLP-OST-2019/stats/stats.full.csv"
 	run:
 		import pandas
 		frames = [ pandas.read_csv(f) for f in input.files ]
-- 
GitLab


From 3395a294974529e5ebc8e750a7ab047a7443a90d Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:35:50 +0100
Subject: [PATCH 18/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 743c801b..c82c0a44 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -243,6 +243,7 @@ def get_score_stats(file, entity):
 
 
 '''
+
 '''
 rule stats_eval_BB19-norm+ner:
 	input:
@@ -266,6 +267,7 @@ rule stats_eval_BB19-norm+ner:
 
 
 '''
+
 '''
 rule stats_eval_BB19-rel+ner:
 	input:
@@ -288,6 +290,7 @@ rule stats_eval_BB19-rel+ner:
 
 
 '''
+
 '''
 rule stats_eval_BB19-kb+ner:
 	input:
-- 
GitLab


From 8dc7cd37f44b9be37315962ea101a973d3492afd Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:41:50 +0100
Subject: [PATCH 19/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index c82c0a44..8dee3107 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -245,7 +245,7 @@ def get_score_stats(file, entity):
 '''
 
 '''
-rule stats_eval_BB19-norm+ner:
+rule stats_eval_BB19-norm:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
@@ -269,7 +269,7 @@ rule stats_eval_BB19-norm+ner:
 '''
 
 '''
-rule stats_eval_BB19-rel+ner:
+rule stats_eval_BB19-rel:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
@@ -292,7 +292,7 @@ rule stats_eval_BB19-rel+ner:
 '''
 
 '''
-rule stats_eval_BB19-kb+ner:
+rule stats_eval_BB19-kb:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-- 
GitLab


From a8e31f00b23800a4037f2126f1397072699a5c77 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:43:28 +0100
Subject: [PATCH 20/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 8dee3107..d5ca3ef7 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -245,7 +245,7 @@ def get_score_stats(file, entity):
 '''
 
 '''
-rule stats_eval_BB19-norm:
+rule stats_eval_BB19_norm:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
@@ -269,7 +269,7 @@ rule stats_eval_BB19-norm:
 '''
 
 '''
-rule stats_eval_BB19-rel:
+rule stats_eval_BB19_rel:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
@@ -292,7 +292,7 @@ rule stats_eval_BB19-rel:
 '''
 
 '''
-rule stats_eval_BB19-kb:
+rule stats_eval_BB19_kb:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-- 
GitLab


From 5e8bef3c8cd6c3bde78f77bc071815f7ea6c17b9 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:44:33 +0100
Subject: [PATCH 21/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index d5ca3ef7..ed649192 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -16,7 +16,7 @@ cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_
 cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
 '''
 ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
-rule stats_cirm:
+rule stats_cirm_BIA:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -40,7 +40,7 @@ cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
+SORTIES_CIRM_Levure = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
 rule stats_cirm:
-- 
GitLab


From ebc1b6b3963bcc3037834b1d52043d3a142f3e32 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:46:17 +0100
Subject: [PATCH 22/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index ed649192..9f2b51a7 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -40,10 +40,10 @@ cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-SORTIES_CIRM_Levure = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
+SORTIES_CIRM= ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
-rule stats_cirm:
+rule stats_cirm_Levure:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -61,6 +61,7 @@ rule stats_cirm:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+
 FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
 '''
 merge
-- 
GitLab


From d9a716abf4f31fed3610089c0d79e6221cd42008 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:34:23 +0100
Subject: [PATCH 23/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index fe279abc..ab0e1c2f 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -22,12 +22,12 @@ pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
-- 
GitLab


From 7c5bd419fe82e147c4be3de09623bc9f2066a06c Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:50:20 +0100
Subject: [PATCH 24/64] Update generate_stats.snakefile,
 corpora/florilege/labels.stats files

---
 corpora/florilege/labels.stats | 2 ++
 generate_stats.snakefile       | 8 +++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index ab0e1c2f..022ffe6b 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -23,10 +23,12 @@ pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-rela
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
 eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
+eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
 eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
 eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
 eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
+eval_BB19-rel+ner_002, score global sur la prédiction de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Standard_scoring
 eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
 eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
 eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9f2b51a7..29d17b67 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -260,10 +260,11 @@ rule stats_eval_BB19_norm:
 		c="line"
 	run:
 		import pandas
+		s = get_score_stats(input.file, "Standard scoring")
 		h = get_score_stats(input.file, "Habitats")
 		p = get_score_stats(input.file, "Phenotypes")
 		m = get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], h['value'], p['value'], m['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -284,9 +285,10 @@ rule stats_eval_BB19_rel:
 		c="line"
 	run:
 		import pandas
+		s = get_score_stats(input.file, "Standard scoring")
 		l = get_score_stats(input.file, "Lives_In")
 		e = get_score_stats(input.file, "Exhibits")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], l['value'], e['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -347,7 +349,7 @@ merge
 rule joint_stats:
 	input:
 		full_r="corpora/florilege/stats.full.csv",
-		concepts="corpora/florilege/stats.labels"
+		concepts="corpora/florilege/labels.stats"
 	output:
 		result="corpora/florilege/full_stats_with_labels.csv"
 	run:
-- 
GitLab


From b98db45f38d0c21afedfb2aff053fef2783fdcdf Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:53:30 +0100
Subject: [PATCH 25/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 29d17b67..f221f73b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -264,7 +264,7 @@ rule stats_eval_BB19_norm:
 		h = get_score_stats(input.file, "Habitats")
 		p = get_score_stats(input.file, "Phenotypes")
 		m = get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -288,7 +288,7 @@ rule stats_eval_BB19_rel:
 		s = get_score_stats(input.file, "Standard scoring")
 		l = get_score_stats(input.file, "Lives_In")
 		e = get_score_stats(input.file, "Exhibits")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
-- 
GitLab


From 14102aea199e3b0939366bfca0934461d0690719 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:14:43 +0000
Subject: [PATCH 26/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 81 ++++++++++++++++++++--------------------
 1 file changed, 40 insertions(+), 41 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index f221f73b..9e49550b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,4 +1,3 @@
-
 '''
 all
 '''
@@ -23,11 +22,11 @@ rule stats_cirm_BIA:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="source",
-		v0="cirm",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="CIRM",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
@@ -50,11 +49,11 @@ rule stats_cirm_Levure:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="source",
-		v0="cirm",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="CIRM",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -94,11 +93,11 @@ rule stats_genbank:
 		stats="corpora/genbank/stats/{file}_stats.csv"
 	params:
 		result="genbank/{file}",
-		c0="source",
-		v0="genbank",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="GENBANK",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -136,11 +135,11 @@ rule stats_dsmz:
 		stats="corpora/dsmz/stats/{file}_stats.csv"
 	params:
 		result="dsmz/{file}",
-		c0="source",
-		v0="dsmz",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="DSMZ",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -188,11 +187,11 @@ rule stats_pubmed:
 		stats="corpora/microbes-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
-		c0="source",
-		v0="pubmed",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="PUBMED",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -253,11 +252,11 @@ rule stats_eval_BB19_norm:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-norm+ner",
-		c0="source",
-		v0="BB19-norm+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-NORM+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -278,11 +277,11 @@ rule stats_eval_BB19_rel:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-rel+ner",
-		c0="source",
-		v0="BB19-rel+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-REL+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -302,11 +301,11 @@ rule stats_eval_BB19_kb:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-kb+ner",
-		c0="source",
-		v0="BB19-kb+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-KB+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
-- 
GitLab


From e44736851f8a8dcb1b9e237bdce630c572c195ad Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:33:20 +0000
Subject: [PATCH 27/64] Update corpora/florilege/stats.labels,
 corpora/florilege/labels.stats, generate_stats.snakefile files

---
 corpora/florilege/labels.stats | 11 ++++++++---
 corpora/florilege/stats.labels |  2 +-
 generate_stats.snakefile       | 32 ++++++++++++++++----------------
 3 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 022ffe6b..b3c55895 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1,16 +1,20 @@
-id,label,file
+id,libelle,uri
+cirm_000, date de mise à jour des données de cirm, /db/maj/genbank/date
 cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
 cirm_002,nombre d'entrées cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
 cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_taxids.txt
 cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
 cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
 cirm_006,nombre d'habitat de cirm-Levure,cirm/mapped_yeast_habitats.txt
+genbank_000, date de mise à jour des données de genbank,/db/maj/genbank/date
 genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
 genbank_002,nombre de taxon de genbank,genbank/mapped_taxids.txt
 genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
+dsmz_000, date de mise à jour des données de dsmz,/db/maj/dsmz/date
 dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
 dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
 dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
+pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
 pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
 pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
 pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
@@ -20,8 +24,8 @@ pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotyp
 pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
 pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
-eval_001, corpus utilisés, BioNLP-OST-2019
-eval_002, date, None
+eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
+eval_002, date d'évaluation, migale/evaluation/BB19/date
 eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
 eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
@@ -33,3 +37,4 @@ eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,Bio
 eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
 eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
 eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
+ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/pubmed/date
diff --git a/corpora/florilege/stats.labels b/corpora/florilege/stats.labels
index 7feb5ea9..3be2a540 100644
--- a/corpora/florilege/stats.labels
+++ b/corpora/florilege/stats.labels
@@ -1,4 +1,4 @@
-label,file
+LIBELLE,file
 entrées cirm,cirm/2019-07-05/extraction_3-fv.csv
 entrées cirm (levure),cirm/Levures_2017/data_CIRM_levures_extraction_09032017.csv
 taxid cirm,cirm/mapped_taxids.txt
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9e49550b..89e36661 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -24,8 +24,8 @@ rule stats_cirm_BIA:
 		result="cirm/{file}",
 		c0="SOURCE",
 		v0="CIRM",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -51,8 +51,8 @@ rule stats_cirm_Levure:
 		result="cirm/{file}",
 		c0="SOURCE",
 		v0="CIRM",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -95,8 +95,8 @@ rule stats_genbank:
 		result="genbank/{file}",
 		c0="SOURCE",
 		v0="GENBANK",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -137,8 +137,8 @@ rule stats_dsmz:
 		result="dsmz/{file}",
 		c0="SOURCE",
 		v0="DSMZ",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -189,8 +189,8 @@ rule stats_pubmed:
 		result="microbes-2019/{file}",
 		c0="SOURCE",
 		v0="PUBMED",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -254,8 +254,8 @@ rule stats_eval_BB19_norm:
 		result="BioNLP-OST-2019/BB19-norm+ner",
 		c0="SOURCE",
 		v0="BB19-NORM+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -279,8 +279,8 @@ rule stats_eval_BB19_rel:
 		result="BioNLP-OST-2019/BB19-rel+ner",
 		c0="SOURCE",
 		v0="BB19-REL+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -303,8 +303,8 @@ rule stats_eval_BB19_kb:
 		result="BioNLP-OST-2019/BB19-kb+ner",
 		c0="SOURCE",
 		v0="BB19-KB+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
-- 
GitLab


From 516972f3c74153efdb15b9cd91c936ffc9ab5ccc Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:36:55 +0000
Subject: [PATCH 28/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 80 ++++++++++++++++++++--------------------
 1 file changed, 40 insertions(+), 40 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 89e36661..33fe8e9a 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -22,11 +22,11 @@ rule stats_cirm_BIA:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="SOURCE",
-		v0="CIRM",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="cirm",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
@@ -49,11 +49,11 @@ rule stats_cirm_Levure:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="SOURCE",
-		v0="CIRM",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="cirm",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -93,11 +93,11 @@ rule stats_genbank:
 		stats="corpora/genbank/stats/{file}_stats.csv"
 	params:
 		result="genbank/{file}",
-		c0="SOURCE",
-		v0="GENBANK",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="genbank",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -135,11 +135,11 @@ rule stats_dsmz:
 		stats="corpora/dsmz/stats/{file}_stats.csv"
 	params:
 		result="dsmz/{file}",
-		c0="SOURCE",
-		v0="DSMZ",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="dsmz",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -187,11 +187,11 @@ rule stats_pubmed:
 		stats="corpora/microbes-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
-		c0="SOURCE",
-		v0="PUBMED",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="pubmed",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -252,11 +252,11 @@ rule stats_eval_BB19_norm:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-norm+ner",
-		c0="SOURCE",
-		v0="BB19-NORM+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-norm+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -277,11 +277,11 @@ rule stats_eval_BB19_rel:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-rel+ner",
-		c0="SOURCE",
-		v0="BB19-REL+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-rel+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -301,11 +301,11 @@ rule stats_eval_BB19_kb:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-kb+ner",
-		c0="SOURCE",
-		v0="BB19-KB+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-kb+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
-- 
GitLab


From c7e202c8dcb5bc0d1da870ff162d06097f4b71d4 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 12:02:34 +0000
Subject: [PATCH 29/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 33fe8e9a..0f3be205 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -355,5 +355,5 @@ rule joint_stats:
 		import pandas
 		df1=pandas.read_csv(input.concepts)
 		df2=pandas.read_csv(input.full_r)
-		df = pandas.merge(df1, df2)
+		df = pandas.merge(df1, df2, on="uri", how="left")
 		df.to_csv(output.result, index=False)
-- 
GitLab


From bca9ac7d89c03a39facf3755d677816e6b9652c9 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mouhamadou.ba@inra.fr>
Date: Thu, 4 Mar 2021 13:19:16 +0100
Subject: [PATCH 30/64] update ontobiotope

---
 ancillaries/BioNLP-OST+EnovFood-Habitat.obo   | 3674 +++++++++++++++-
 ancillaries/BioNLP-OST+EnovFood-Phenotype.obo |   16 +-
 .../BioNLP-OST+EnovFood-no-obsolete.obo       | 3687 ++++++++++++++++-
 3 files changed, 7269 insertions(+), 108 deletions(-)

diff --git a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo b/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
index 279bda6a..5ac41ce6 100644
--- a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000001
@@ -224,6 +223,7 @@ is_a: OBT:000006 ! artificial environment
 [Term]
 id: OBT:000067
 name: cultivated habitat
+synonym: "cultivated area" EXACT []
 is_a: OBT:000004 ! animal husbandry and agricultural habitat
 
 [Term]
@@ -722,7 +722,7 @@ is_a: OBT:000156 ! subterrestrial habitat
 [Term]
 id: OBT:000226
 name: ceiling tile
-is_a: OBT:000098 ! household good
+is_a: OBT:003617 ! environmental surface
 
 [Term]
 id: OBT:000227
@@ -1322,7 +1322,7 @@ is_a: OBT:000094 ! food for human
 
 [Term]
 id: OBT:000398
-name: prothesis
+name: prosthesis
 is_a: OBT:000108 ! medical equipment
 
 [Term]
@@ -1354,6 +1354,7 @@ is_a: OBT:000093 ! fish pond
 id: OBT:000407
 name: respiratory tract
 synonym: "respiratory" RELATED [TyDI:55563]
+synonym: "respiratory airway" RELATED []
 synonym: "respiratory tree" RELATED [TyDI:55564]
 is_a: OBT:000039 ! animal part
 
@@ -1476,6 +1477,7 @@ is_a: OBT:000110 ! medical sample
 id: OBT:000432
 name: starter culture
 synonym: "dry starter" RELATED [TyDI:52942]
+synonym: "starter" EXACT []
 is_a: OBT:000113 ! microflora
 
 [Term]
@@ -1698,6 +1700,7 @@ is_a: OBT:000190 ! anaerobic bioreactor
 [Term]
 id: OBT:000488
 name: anaerobic sludge blanket reactor
+synonym: "UASB reactor" EXACT []
 is_a: OBT:000190 ! anaerobic bioreactor
 
 [Term]
@@ -1748,7 +1751,7 @@ is_a: OBT:000332 ! lesion
 [Term]
 id: OBT:000498
 name: auricular prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000500
@@ -1773,6 +1776,7 @@ is_a: OBT:000208 ! bathroom equipment
 [Term]
 id: OBT:000504
 name: bathtub
+synonym: "bath tub" EXACT []
 is_a: OBT:000208 ! bathroom equipment
 
 [Term]
@@ -1888,7 +1892,7 @@ is_a: OBT:000340 ! meat and bone meal
 [Term]
 id: OBT:000528
 name: bone-anchored prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000529
@@ -2064,7 +2068,7 @@ is_a: OBT:000338 ! marine environment
 id: OBT:000564
 name: cochlear prosthesis
 synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003645 ! ocular prosthesis
 
 [Term]
 id: OBT:000565
@@ -2100,7 +2104,7 @@ is_a: OBT:000240 ! commodity and primary derivative thereof
 [Term]
 id: OBT:000571
 name: compost
-is_a: OBT:000365 ! organic matter
+is_a: OBT:000585 ! dead matter
 
 [Term]
 id: OBT:000572
@@ -2151,6 +2155,7 @@ is_a: OBT:000194 ! animal farm
 [Term]
 id: OBT:000584
 name: dairy starter culture
+synonym: "dairy starter" EXACT []
 is_a: OBT:000432 ! starter culture
 
 [Term]
@@ -2188,8 +2193,8 @@ is_a: OBT:000313 ! host associated biofilm
 
 [Term]
 id: OBT:000591
-name: dental prothesis
-is_a: OBT:000398 ! prothesis
+name: dental prosthesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000592
@@ -2661,7 +2666,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000701
 name: laryngeal prosthetic device
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000702
@@ -2758,11 +2763,13 @@ is_a: OBT:000364 ! organ
 [Term]
 id: OBT:000720
 name: maize feed
+synonym: "corn feed" NARROW []
 is_a: OBT:000229 ! cereal feed
 
 [Term]
 id: OBT:000721
 name: maize storage
+synonym: "corn storage" NARROW []
 is_a: OBT:000423 ! silo
 
 [Term]
@@ -2807,7 +2814,7 @@ is_a: OBT:000341 ! medical outfit
 
 [Term]
 id: OBT:000730
-name: membrane
+name: animal membrane
 is_a: OBT:000196 ! animal tissue
 
 [Term]
@@ -3003,7 +3010,7 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000786
 name: pacemaker
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003632 ! prosthetic cardiac device
 
 [Term]
 id: OBT:000787
@@ -3180,7 +3187,8 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000830
 name: prosthetic joint
-is_a: OBT:000398 ! prothesis
+synonym: "joint prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000831
@@ -3725,7 +3733,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000947
 name: veterinary drug
-is_a: OBT:000261 ! drug
+is_a: OBT:003680 ! veterinary product
 
 [Term]
 id: OBT:000948
@@ -4929,6 +4937,7 @@ is_a: OBT:000684 ! industrial equipment
 [Term]
 id: OBT:001190
 name: maize silage
+synonym: "corn silage" NARROW []
 is_a: OBT:000871 ! silage
 
 [Term]
@@ -4988,7 +4997,7 @@ is_a: OBT:000816 ! plant tissue
 [Term]
 id: OBT:001202
 name: mesentery
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001206
@@ -5058,7 +5067,7 @@ is_a: OBT:000710 ! lining
 id: OBT:001219
 name: mucous membrane
 synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001220
@@ -5229,7 +5238,7 @@ is_a: OBT:000642 ! gastrointestinal tract part
 [Term]
 id: OBT:001253
 name: peritoneum
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001254
@@ -5747,6 +5756,7 @@ is_a: OBT:000529 ! broncho-pulmonary segment
 id: OBT:001359
 name: treated wood
 is_a: OBT:000586 ! dead wood
+is_a: OBT:003742 ! wood waste
 
 [Term]
 id: OBT:001360
@@ -5877,7 +5887,7 @@ is_a: OBT:000694 ! invertebrate species
 [Term]
 id: OBT:001387
 name: yolk sac
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001388
@@ -6165,6 +6175,7 @@ is_a: OBT:001038 ! clean room
 [Term]
 id: OBT:001445
 name: birch
+synonym: "birch tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -6673,11 +6684,6 @@ id: OBT:001544
 name: eosinophil
 is_a: OBT:001134 ! granulocyte
 
-[Term]
-id: OBT:001545
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-
 [Term]
 id: OBT:001546
 name: fermented food
@@ -6746,6 +6752,7 @@ is_a: OBT:001097 ! factory
 [Term]
 id: OBT:001558
 name: food processing waste
+synonym: "food residue" RELATED []
 is_a: OBT:001157 ! industrial organic waste
 
 [Term]
@@ -6793,7 +6800,8 @@ is_a: OBT:001114 ! food rind
 [Term]
 id: OBT:001567
 name: fruit tree
-is_a: OBT:001360 ! tree
+comment: horticole meaning
+is_a: OBT:002699 ! cultivated plant
 
 [Term]
 id: OBT:001568
@@ -7300,6 +7308,7 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 [Term]
 id: OBT:001666
 name: oak
+synonym: "oak tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -7548,7 +7557,7 @@ is_a: OBT:001257 ! plankton
 [Term]
 id: OBT:001715
 name: pine forest
-is_a: OBT:001119 ! forest
+is_a: OBT:003881 ! conifer forest
 
 [Term]
 id: OBT:001716
@@ -7562,8 +7571,9 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 
 [Term]
 id: OBT:001718
-name: plant residue
-is_a: OBT:001258 ! plant material
+name: agricultural plant residue
+synonym: "agricultural plant waste" NARROW []
+is_a: OBT:000478 ! agricultural waste
 
 [Term]
 id: OBT:001719
@@ -7592,7 +7602,7 @@ is_a: OBT:001132 ! grain and primary derivative thereof
 
 [Term]
 id: OBT:001724
-name: potato
+name: potato plant
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -8007,8 +8017,8 @@ is_a: OBT:001045 ! confectionery
 
 [Term]
 id: OBT:001803
-name: sugar-beet
-synonym: "betroot" EXACT [TyDI:49625]
+name: sugar-beet plant
+synonym: "betroot plant" EXACT [TyDI:49625]
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -8085,7 +8095,8 @@ is_a: OBT:001159 ! industrial sludge
 
 [Term]
 id: OBT:001818
-name: textile industry
+name: textile mill
+synonym: "textile factory" NARROW []
 is_a: OBT:001097 ! factory
 
 [Term]
@@ -8943,8 +8954,9 @@ is_a: OBT:001621 ! livestock barn
 
 [Term]
 id: OBT:001988
-name: dairy industry
-synonym: "milk industry" RELATED [TyDI:55159]
+name: dairy processing plant
+synonym: "dairy factory" EXACT []
+synonym: "milk processing factory" RELATED [TyDI:55159]
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9170,7 +9182,7 @@ is_a: OBT:001446 ! bird
 
 [Term]
 id: OBT:002039
-name: food fermentation industry
+name: food fermentation factory
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9350,7 +9362,7 @@ is_a: OBT:001821 ! tick
 [Term]
 id: OBT:002073
 name: hay
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002074
@@ -9418,7 +9430,7 @@ is_a: OBT:001557 ! food processing factory
 id: OBT:002086
 name: industrial bakery
 synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:003759 ! bakery
 
 [Term]
 id: OBT:002087
@@ -9635,7 +9647,7 @@ is_a: OBT:001802 ! sugar confectionery
 
 [Term]
 id: OBT:002129
-name: meat industry
+name: meat processing plant
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9940,7 +9952,7 @@ is_a: OBT:001717 ! pistachio and primary derivative thereof
 [Term]
 id: OBT:002190
 name: plant cutting
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002191
@@ -10102,7 +10114,7 @@ is_a: OBT:001744 ! rice based dish
 [Term]
 id: OBT:002225
 name: rice-plant residue
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002226
@@ -10237,7 +10249,7 @@ id: OBT:002251
 name: slaughter plant
 synonym: "abattoir" RELATED [TyDI:50262]
 synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:002129 ! meat processing plant
 
 [Term]
 id: OBT:002252
@@ -10344,7 +10356,7 @@ is_a: OBT:001556 ! food fermentation equipment
 [Term]
 id: OBT:002271
 name: straw
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002272
@@ -10829,7 +10841,7 @@ is_a: OBT:002018 ! environmental water with chemical property
 [Term]
 id: OBT:002372
 name: brewery
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:002373
@@ -11039,7 +11051,7 @@ is_a: OBT:002174 ! pastry product
 [Term]
 id: OBT:002414
 name: creamery
-is_a: OBT:001988 ! dairy industry
+is_a: OBT:001988 ! dairy processing plant
 
 [Term]
 id: OBT:002415
@@ -11506,6 +11518,7 @@ is_a: OBT:002126 ! marine fish meat
 [Term]
 id: OBT:002513
 name: maize
+synonym: "corn" NARROW []
 is_a: OBT:002120 ! maize and primary derivative thereof
 
 [Term]
@@ -12747,7 +12760,7 @@ name: endothelium
 synonym: "endothelial" RELATED [TyDI:52445]
 synonym: "vascular endothelium" EXACT [TyDI:52444]
 is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:002791
@@ -13150,6 +13163,7 @@ is_a: OBT:000710 ! lining
 [Term]
 id: OBT:002914
 name: maize plant
+synonym: "corn plant" NARROW []
 is_a: OBT:002771 ! cereal crop
 
 [Term]
@@ -13490,6 +13504,7 @@ name: hotspring
 synonym: "hot spring" EXACT [TyDI:49581]
 is_a: OBT:000625 ! extreme high temperature environment
 is_a: OBT:001333 ! spring
+is_a: OBT:002019 ! environmental water with physical property
 
 [Term]
 id: OBT:002992
@@ -14078,7 +14093,7 @@ is_a: OBT:001632 ! market garden plant
 
 [Term]
 id: OBT:003098
-name: gum margin
+name: gingival margin
 is_a: OBT:003055 ! gum tissue
 
 [Term]
@@ -14764,7 +14779,7 @@ id: OBT:003221
 name: peritrophic membrane
 is_a: OBT:000200 ! arthropod part
 is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:003222
@@ -14941,8 +14956,8 @@ is_a: OBT:002055 ! fungi as food
 [Term]
 id: OBT:003251
 name: cheese factory
-is_a: OBT:001988 ! dairy industry
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:001988 ! dairy processing plant
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:003252
@@ -15028,6 +15043,7 @@ is_a: OBT:003203 ! heavy metal contaminated soil
 id: OBT:003266
 name: mine waste water
 synonym: "mine wastewater" EXACT [TyDI:51583]
+synonym: "mine water" EXACT []
 is_a: OBT:001212 ! mine waste
 is_a: OBT:002754 ! waste water
 
@@ -16195,7 +16211,7 @@ is_a: OBT:003458 ! semi soft cheese
 
 [Term]
 id: OBT:003475
-name: Granular
+name: Granular cheese
 is_a: OBT:003450 ! hard cheese
 
 [Term]
@@ -16902,3 +16918,3561 @@ name: tejuino
 synonym: "tejuíno" EXACT [TyDI:51685]
 is_a: OBT:003410 ! corn beverage
 is_a: OBT:003596 ! fermented juice
+
+[Term]
+id: OBT:003602
+name: airway epithelium
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003603
+name: chicken breast meat
+is_a: OBT:002394 ! chicken meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003604
+name: turkey breast meat
+is_a: OBT:002631 ! turkey meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003605
+name: rice bran
+is_a: OBT:001458 ! bran
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003606
+name: lacrimal sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003607
+name: conjunctival sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003608
+name: aneurysmal sac
+synonym: "aneurysm sac" EXACT []
+synonym: "aortic sac" EXACT []
+is_a: OBT:000231 ! circulatory system part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003609
+name: abdominal air sac
+synonym: "air sac" EXACT []
+synonym: "thoracic air sac" EXACT []
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003610
+name: hernial sac
+is_a: OBT:000039 ! animal part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003611
+name: umbilical cord
+is_a: OBT:000463 ! urogenital tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003612
+name: umbilical cord blood
+is_a: OBT:000521 ! blood
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003613
+name: vocal cord
+is_a: OBT:000529 ! broncho-pulmonary segment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003615
+name: box lunch
+is_a: OBT:000788 ! packed lunch
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003617
+name: environmental surface
+is_a: OBT:000006 ! artificial environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003618
+name: ceramic tile
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003619
+name: ceramic wall tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003620
+name: ceramic roofing tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003621
+name: stainless steel surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003622
+name: PCV surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003623
+name: plasticized PVC
+synonym: "PVC plastic" NARROW []
+is_a: OBT:003622 ! PCV surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003624
+name: PVC film
+is_a: OBT:000787 ! packaging
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003625
+name: sealed concrete
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003626
+name: bamboo cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003627
+name: wood Cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003628
+name: plastic cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003629
+name: voice prosthesis
+is_a: OBT:003630 ! tracheoesophageal prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003630
+name: tracheoesophageal prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003631
+name: silicone rubber voice prosthesis
+is_a: OBT:003629 ! voice prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003632
+name: prosthetic cardiac device
+synonym: "intracardiac prosthesis" NARROW []
+synonym: "prosthetic cardiovascular device" NARROW []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003633
+name: prosthetic heart valve
+synonym: "heart valve prosthesis" NARROW []
+synonym: "prosthetic valve" NARROW []
+synonym: "valvular prosthesis" NARROW []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003634
+name: mitral valve prosthesis
+synonym: "mitral prosthesis" EXACT []
+is_a: OBT:003633 ! prosthetic heart valve
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003635
+name: aortic prosthetic valve
+synonym: "aortic valve prosthesis" EXACT []
+synonym: "arterial prosthesis" EXACT []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003636
+name: orthopedic prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003637
+name: othopedic implant
+is_a: OBT:003636 ! orthopedic prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003638
+name: hip prosthesis
+synonym: "prosthetic hip joint" EXACT []
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003639
+name: femoral prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003640
+name: knee prosthesis
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003641
+name: shoulder prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003642
+name: cranial prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003643
+name: penile prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003644
+name: testicular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003645
+name: ocular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003646
+name: prosthetic eye
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003647
+name: iris prosthesis
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003648
+name: orbital implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003649
+name: cochlear implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003650
+name: dental implant
+is_a: OBT:000591 ! dental prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003651
+name: palatal obturator prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003652
+name: breast prosthesis
+synonym: "mammary prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003653
+name: breast implant
+is_a: OBT:003652 ! breast prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003654
+name: suction-socket prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003655
+name: granular sludge
+is_a: OBT:001523 ! digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003656
+name: aerobic granular sludge
+is_a: OBT:001861 ! anaerobic digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003657
+name: aerobic granular sludge reactor
+synonym: "AGS reactor" EXACT []
+is_a: OBT:000180 ! aerobic bioreactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003658
+name: granular sludge bed reactor
+synonym: "EGSB reactor" EXACT []
+is_a: OBT:000488 ! anaerobic sludge blanket reactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003659
+name: public swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003660
+name: indoor swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003661
+name: shower bath
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003662
+name: public bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003663
+name: traditional public bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003664
+name: bath basin
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003665
+name: thermal bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003666
+name: thermal saline bath
+is_a: OBT:002592 ! saline water
+is_a: OBT:003665 ! thermal bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003667
+name: mineral bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003668
+name: spa bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003669
+name: seawater bath
+is_a: OBT:003105 ! marine water
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003670
+name: freshwater bath
+is_a: OBT:002455 ! freshwater
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003671
+name: open air bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003672
+name: spring bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003673
+name: hot water bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003674
+name: hot spring bath
+is_a: OBT:002990 ! hotspring
+is_a: OBT:003673 ! hot water bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003675
+name: hot spring spa bath
+is_a: OBT:003674 ! hot spring bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003676
+name: bath sponge
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003677
+name: bath tub heating
+is_a: OBT:000671 ! home heating system
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003678
+name: antiseptic bath
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003679
+name: chlorhexidine bath
+is_a: OBT:003678 ! antiseptic bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003680
+name: veterinary product
+is_a: OBT:000011 ! medical environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003681
+name: insecticide bath
+is_a: OBT:003680 ! veterinary product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003682
+name: antiseptic shower
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003683
+name: dyeing bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003684
+name: skin tannery bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003685
+name: bleach bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003689
+name: mango tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003690
+name: lemon tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003691
+name: peach tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003692
+name: apricot tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003693
+name: quince tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003694
+name: cherry tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003695
+name: khaki tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003696
+name: lime tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003697
+name: carrot plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003698
+name: broccoli plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003699
+name: brussel sprout plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003700
+name: chinese cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003701
+name: collard green plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003702
+name: head cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003703
+name: shallot plant
+is_a: OBT:001389 ! Allium
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003704
+name: fruiting vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003705
+name: courgette plant
+synonym: "zucchini plant" EXACT []
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003706
+name: cucumber plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003707
+name: gherkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003708
+name: melon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003709
+name: pumpkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003710
+name: sweet pepper plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003711
+name: watermelon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003712
+name: leafy vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003713
+name: celery plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003714
+name: spinach plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003715
+name: table water
+is_a: OBT:001530 ! drinking water
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003716
+name: garment factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003717
+name: dyeing factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003718
+name: traditional Chinese fermented cabbage
+is_a: OBT:002321 ! Chinese cabbage
+is_a: OBT:003096 ! fermented vegetable product
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003719
+name: nasal swab
+is_a: OBT:001228 ! nasal secretion
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003720
+name: rum factory
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003721
+name: whisky distillery
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003722
+name: liquor
+is_a: OBT:001397 ! alcoholic drink
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003723
+name: udder
+is_a: OBT:000723 ! mammalian part
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003724
+name: lactic starter
+is_a: OBT:000584 ! dairy starter culture
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003726
+name: plant residue from food processing
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003727
+name: grape pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003728
+name: apple pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003729
+name: olive pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003730
+name: grape must
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003731
+name: sugarcane bagasse
+synonym: "sugar cane bagasse" EXACT []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003732
+name: agave bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003733
+name: citrus bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003734
+name: soy bran
+is_a: OBT:000038 ! animal feed
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003735
+name: palm kernel press cake
+synonym: "residue from palm oil extraction" NARROW []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003736
+name: sugar beet pressed pulp
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003737
+name: cranberry press cake
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003738
+name: forage residue
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003739
+name: cotton plant waste
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003740
+name: cottonseed hull
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003741
+name: olive press cake
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003742
+name: wood waste
+is_a: OBT:000467 ! waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003743
+name: sawdust
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003744
+name: waste house wood
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003745
+name: construction wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003746
+name: demolition wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003747
+name: hazardous industrial waste
+is_a: OBT:000685 ! industrial waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003748
+name: agricultural woody waste
+is_a: OBT:000478 ! agricultural waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003749
+name: wood waste fiber
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003750
+name: transport structure
+is_a: OBT:000162 ! transport equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003751
+name: pallet
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003752
+name: shipping container
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003753
+name: wooden pallet
+is_a: OBT:003751 ! pallet
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003756
+name: wood barrel
+is_a: OBT:000434 ! storage equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003757
+name: oak barrel
+is_a: OBT:003756 ! wood barrel
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003759
+name: bakery
+is_a: OBT:001557 ! food processing factory
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003760
+name: traditional bakery
+is_a: OBT:003759 ! bakery
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003761
+name: traditional dairy
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003762
+name: dairy farm
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003763
+name: snowpack
+is_a: OBT:000881 ! snow
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003764
+name: conifer needle
+is_a: OBT:000807 ! phylloplane part
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003765
+name: agricultural fence
+is_a: OBT:001183 ! livestock habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003766
+name: ungulate
+is_a: OBT:002078 ! herbivore
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003767
+name: biome type forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003768
+name: alpine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003769
+name: tropical rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003770
+name: arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003771
+name: boreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003772
+name: coastal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003773
+name: cooler rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003774
+name: dune forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003775
+name: equatorial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003776
+name: montane forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003777
+name: hemiboreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003778
+name: high altitude forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003779
+name: humid lakeland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003780
+name: low mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003781
+name: subtropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003782
+name: taiga forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003783
+name: lowland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003784
+name: marshy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003785
+name: mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003786
+name: neotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003787
+name: paleotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003788
+name: savannah - forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003789
+name: subalpine forest
+synonym: "sub-alpine forest" EXACT []
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003790
+name: sub-Antarctic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003791
+name: warm sub-tropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003792
+name: dry forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003793
+name: semi - arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003794
+name: semiarid temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003795
+name: hill forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003796
+name: hot forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003797
+name: humid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003798
+name: inland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003799
+name: moist forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003800
+name: plain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003801
+name: pluvial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003802
+name: riverbank forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003803
+name: riverine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003804
+name: submerged forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003805
+name: temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003806
+name: underwater forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003807
+name: upland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003808
+name: volcanic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003809
+name: warm - temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003810
+name: wet forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003811
+name: wildland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003812
+name: drained forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003813
+name: soddy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003814
+name: natural and managed forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003815
+name: natural forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003816
+name: virgin forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003817
+name: uncontrolled forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003818
+name: undisturbed forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003819
+name: unmanaged forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003820
+name: unpolluted forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003821
+name: preserved forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003822
+name: protected forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003823
+name: native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003824
+name: intact forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003825
+name: primary forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003826
+name: primeval forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003827
+name: pristine area of native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003828
+name: pristine forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003829
+name: non-burnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003830
+name: unburnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003831
+name: managed forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
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+name: man - made forest system
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003833
+name: municipal forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003834
+name: park forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003836
+name: periurban forest
+synonym: "peri-urban" EXACT []
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003837
+name: plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003838
+name: recreational forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
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+name: reserve forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
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+name: rural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003841
+name: semi-natural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003842
+name: suburban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003843
+name: urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003844
+name: village-adjacent forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003845
+name: village forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003846
+name: wood forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
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+name: second-growth forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003848
+name: secondary forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003849
+name: early successional forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003850
+name: burnt forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003851
+name: artificial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003852
+name: commercial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003853
+name: commercial plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003854
+name: community forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003855
+name: disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003856
+name: disturbed urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003857
+name: historical forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003858
+name: human disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003859
+name: old forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003860
+name: mature forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003861
+name: mature forest of high conservation value
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003862
+name: mature old-growth forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003863
+name: young forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003864
+name: forest of given species
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003865
+name: alder forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003866
+name: angiosperm-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003867
+name: arboreal forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003868
+name: argan forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003869
+name: aspen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003870
+name: beach forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003871
+name: beech forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003872
+name: beech-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003873
+name: birch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003874
+name: boreonemoral forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003875
+name: bosque forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003876
+name: broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003877
+name: broadleaf forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003878
+name: Cercocarpus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003879
+name: chestnut forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003880
+name: cloud forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003881
+name: conifer forest
+synonym: "coniferous forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003883
+name: coppice forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003884
+name: cypress forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003885
+name: deciduous forest
+synonym: "deciduous specie forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003886
+name: deciduous dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003888
+name: herb-rich coniferous forest
+is_a: OBT:003881 ! conifer forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003890
+name: dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003892
+name: evergreen broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003893
+name: forest with dominant vegetation
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003894
+name: hardwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003896
+name: holm-oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003897
+name: kelp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003898
+name: larch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003899
+name: lucidophyllous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003900
+name: mangrove forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003901
+name: maple forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003902
+name: maso bamboo forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003903
+name: hemlock fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003904
+name: amabilis fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003906
+name: monodominant forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003907
+name: monospecific forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003908
+name: spruce forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003909
+name: Nothofagaceae forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003910
+name: Nothofagus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003911
+name: oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003912
+name: oak-hickory forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003914
+name: ombrophilous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003916
+name: papyrifera forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003917
+name: perennial forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003918
+name: riparian forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003919
+name: pure forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003920
+name: red pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003921
+name: redwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003922
+name: riparian woodland
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003923
+name: poplar forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003924
+name: sclerophyll forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003925
+name: seasonal dry tropical forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003926
+name: scrub forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003927
+name: semi-evergreen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003928
+name: semideciduous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003929
+name: stone pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003931
+name: tanoak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003932
+name: xeric forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003933
+name: xerophytic forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003934
+name: mix forest
+synonym: "mixed forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003935
+name: papilionoid legume tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003936
+name: leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003937
+name: tulip tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003938
+name: tea-oil tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003939
+name: tea plant
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003940
+name: Syzygiumcordatum tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003941
+name: shea butter tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003942
+name: rubber tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003943
+name: riparian tree specie
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003944
+name: Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003945
+name: Prosopis tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003946
+name: peepal tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003947
+name: Pandanus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003948
+name: pacara earpod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003949
+name: Olea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003950
+name: Nothofagus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003951
+name: mopane tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003952
+name: Masson pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003953
+name: manuka tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003954
+name: loquat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003955
+name: lodgepole pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003956
+name: lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003957
+name: Katsura tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003958
+name: kassod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003959
+name: Hippophae tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003960
+name: dipterocarp tree
+synonym: "Dipterocarpaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003961
+name: Dekopon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003962
+name: cycad tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003963
+name: cupuassu tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003964
+name: cupressaceous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003965
+name: chitalpa tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003966
+name: chinquapin tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003967
+name: Casuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003968
+name: Ascomycota tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003969
+name: Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003970
+name: Allocasuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003971
+name: South-African Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003972
+name: African leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003973
+name: willow tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003974
+name: wild tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003976
+name: whitebark pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003977
+name: White spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003978
+name: white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003979
+name: white oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003980
+name: walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003981
+name: urban tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003982
+name: Ulmus nigra tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003983
+name: Ulmus Dodoens Elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003984
+name: turkey oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003985
+name: tung tree
+synonym: "tung oil tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003986
+name: tanoak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003987
+name: Talh tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003988
+name: sycamore tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003989
+name: sweet chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003990
+name: Swedish spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003991
+name: sudden oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003992
+name: stone pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003993
+name: silver birch
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003994
+name: silk oak
+synonym: "silk oak tree" EXACT []
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003995
+name: Sebertia acuminata
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003996
+name: scot pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003997
+name: riparian Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003998
+name: Rhodococcus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003999
+name: redwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004001
+name: radiata pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004002
+name: Quercus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004003
+name: pygmy tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004004
+name: prunus tree
+synonym: "Prunus spp. tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004005
+name: poplar tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004006
+name: ponderosa pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004007
+name: pomegranate tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004008
+name: pome tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004009
+name: poison oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004010
+name: pistachio tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004011
+name: pinyon pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004012
+name: persimmon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004013
+name: persian walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004014
+name: pepper tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004015
+name: pecan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004016
+name: Paulownia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004017
+name: palm tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004018
+name: ornamental tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004019
+name: ornamental Prunus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004020
+name: orchard tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004021
+name: Gingko tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004022
+name: nutmeg tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004023
+name: nutgall tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004024
+name: norway spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004025
+name: North American white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004026
+name: North American oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004027
+name: needled white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004028
+name: needle pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004029
+name: Monterey pine
+synonym: "insignis pine" EXACT []
+synonym: "radiata pine" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004030
+name: Mongolian pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004031
+name: medlar tree
+synonym: "Mespilus germanica" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004032
+name: Mediterranean oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004033
+name: Maritime pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004034
+name: mangrove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004035
+name: litchi tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004036
+name: laurel tree
+synonym: "Lauraceae tree" EXACT []
+synonym: "lauraceous tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004037
+name: Larix sibirica tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004038
+name: larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004039
+name: kraft pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004040
+name: Korean native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004041
+name: Korean lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004042
+name: Korean fir tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004043
+name: Korea spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004044
+name: kiwifruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004045
+name: khat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004046
+name: jujube tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004047
+name: Juglandaceae walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004048
+name: Japanese Yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004049
+name: Japanese larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004050
+name: jack pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004051
+name: Indian yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004052
+name: Indian oak tree
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004053
+name: Indian cork tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004054
+name: Iberian oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004055
+name: holm oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004056
+name: Himalayan pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004057
+name: hazelnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004058
+name: guava tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004059
+name: grapefruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004060
+name: Garry oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004061
+name: Garcinia schomdurgkiana Pierre tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004062
+name: evergreen oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004063
+name: European white elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004064
+name: European hackberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004065
+name: European elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004066
+name: eucalyptus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004067
+name: English oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004068
+name: Engelmann spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004069
+name: Emory oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004070
+name: Eastern cottonwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004071
+name: Dutch elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004072
+name: deciduous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004073
+name: cypress tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004074
+name: cotton tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004075
+name: Azerbaijani almond tree
+is_a: OBT:001402 ! almond tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004076
+name: coffee tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004077
+name: coconut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004078
+name: cocoa tree
+synonym: "chocolate tree" EXACT []
+synonym: "Theobroma cacao" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004079
+name: clove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004080
+name: clementine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004081
+name: chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004082
+name: Cherry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004083
+name: carob tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004084
+name: camellia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004085
+name: brazil nut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004086
+name: blueberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004087
+name: black oak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004088
+name: Bishop pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004090
+name: Betula tree
+synonym: "Betulaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004091
+name: Betula pendula tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004092
+name: beech tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004093
+name: banyan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004094
+name: avocado tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004095
+name: Austrian pine
+synonym: "Austrian pine tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004096
+name: Australian native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004097
+name: Australian native Grey Box tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004098
+name: Australian Hibiscus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004099
+name: Aspen tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004100
+name: argan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004101
+name: Alep pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004102
+name: ald tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004103
+name: acerola tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004104
+name: acacia tree
+synonym: "acacia" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004106
+name: orchad
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004107
+name: planthopper
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004108
+name: jumping plant lice
+synonym: "Psyllidae" NARROW []
+synonym: "psyllids" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004109
+name: sap-feeding insect
+synonym: "sap-sucking insect" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004110
+name: sentinel plant
+is_a: OBT:000912 ! terrestrial plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004111
+name: peony
+is_a: OBT:004110 ! sentinel plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004112
+name: piercing-sucking insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004113
+name: Myzus persicae
+synonym: "green peach aphid" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004114
+name: cabbage aphid
+synonym: "Brevicoryne brassicae" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004115
+name: phytophagous insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004116
+name: cotton boll worm
+synonym: "Helicoverpa armigera" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004117
+name: black cut worm
+synonym: "Agrotis ipsilon" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004118
+name: cotton leaf worm
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004119
+name: rice yellow stem borer
+synonym: "Scirpophaga incertulas" EXACT []
+is_a: OBT:001652 ! moth
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004120
+name: Asian citrus psyllid
+synonym: "Diaphorina citri" EXACT []
+is_a: OBT:004108 ! jumping plant lice
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004121
+name: vineyard
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004122
+name: Graphocephala versuta
+is_a: OBT:002248 ! sharpshooter
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004123
+name: xylem sap-feeding insect
+is_a: OBT:004109 ! sap-feeding insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:009115
+name: palm forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
diff --git a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo b/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
index 86297a0d..05d3f686 100644
--- a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000002
@@ -55,7 +54,7 @@ is_a: OBT:000002 ! microbial phenotype
 
 [Term]
 id: OBT:000024
-name: phenotypre wrt genetic
+name: phenotype wrt genetic
 is_a: OBT:000002 ! microbial phenotype
 
 [Term]
@@ -216,7 +215,7 @@ is_a: OBT:000021 ! phenotype wrt motility
 [Term]
 id: OBT:000118
 name: mutant
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000120
@@ -393,7 +392,7 @@ is_a: OBT:000017 ! phenotype wrt environment
 id: OBT:000169
 name: wild-type
 synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000172
@@ -2340,3 +2339,10 @@ name: chemolithoheterotroph
 synonym: "chemo lithoheterotroph " EXACT [TyDI:54334]
 is_a: OBT:002895 ! chemoheterotroph
 is_a: OBT:002896 ! chemolithotroph
+
+[Term]
+id: OBT:003614
+name: cord-shaped
+is_a: OBT:000386 ! phenotype wrt shape
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
diff --git a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo b/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
index ed2e6ac0..9a9716d4 100644
--- a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000000
@@ -128,7 +127,7 @@ is_a: OBT:000002 ! microbial phenotype
 
 [Term]
 id: OBT:000024
-name: phenotypre wrt genetic
+name: phenotype wrt genetic
 is_a: OBT:000002 ! microbial phenotype
 
 [Term]
@@ -356,6 +355,7 @@ is_a: OBT:000006 ! artificial environment
 [Term]
 id: OBT:000067
 name: cultivated habitat
+synonym: "cultivated area" EXACT []
 is_a: OBT:000004 ! animal husbandry and agricultural habitat
 
 [Term]
@@ -631,7 +631,7 @@ is_a: OBT:000021 ! phenotype wrt motility
 [Term]
 id: OBT:000118
 name: mutant
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000119
@@ -906,7 +906,7 @@ is_a: OBT:000009 ! habitat wrt chemico-physical property
 id: OBT:000169
 name: wild-type
 synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000170
@@ -1210,7 +1210,7 @@ is_a: OBT:000156 ! subterrestrial habitat
 [Term]
 id: OBT:000226
 name: ceiling tile
-is_a: OBT:000098 ! household good
+is_a: OBT:003617 ! environmental surface
 
 [Term]
 id: OBT:000227
@@ -2105,7 +2105,7 @@ is_a: OBT:000094 ! food for human
 
 [Term]
 id: OBT:000398
-name: prothesis
+name: prosthesis
 is_a: OBT:000108 ! medical equipment
 
 [Term]
@@ -2152,6 +2152,7 @@ is_a: OBT:000093 ! fish pond
 id: OBT:000407
 name: respiratory tract
 synonym: "respiratory" RELATED [TyDI:55563]
+synonym: "respiratory airway" RELATED []
 synonym: "respiratory tree" RELATED [TyDI:55564]
 is_a: OBT:000039 ! animal part
 
@@ -2284,6 +2285,7 @@ is_a: OBT:000110 ! medical sample
 id: OBT:000432
 name: starter culture
 synonym: "dry starter" RELATED [TyDI:52942]
+synonym: "starter" EXACT []
 is_a: OBT:000113 ! microflora
 
 [Term]
@@ -2574,6 +2576,7 @@ is_a: OBT:000190 ! anaerobic bioreactor
 [Term]
 id: OBT:000488
 name: anaerobic sludge blanket reactor
+synonym: "UASB reactor" EXACT []
 is_a: OBT:000190 ! anaerobic bioreactor
 
 [Term]
@@ -2624,7 +2627,7 @@ is_a: OBT:000332 ! lesion
 [Term]
 id: OBT:000498
 name: auricular prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000499
@@ -2654,6 +2657,7 @@ is_a: OBT:000208 ! bathroom equipment
 [Term]
 id: OBT:000504
 name: bathtub
+synonym: "bath tub" EXACT []
 is_a: OBT:000208 ! bathroom equipment
 
 [Term]
@@ -2785,7 +2789,7 @@ is_a: OBT:000340 ! meat and bone meal
 [Term]
 id: OBT:000528
 name: bone-anchored prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000529
@@ -2978,7 +2982,7 @@ is_a: OBT:000228 ! cellular shape phenotype
 id: OBT:000564
 name: cochlear prosthesis
 synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003645 ! ocular prosthesis
 
 [Term]
 id: OBT:000565
@@ -3014,7 +3018,7 @@ is_a: OBT:000240 ! commodity and primary derivative thereof
 [Term]
 id: OBT:000571
 name: compost
-is_a: OBT:000365 ! organic matter
+is_a: OBT:000585 ! dead matter
 
 [Term]
 id: OBT:000572
@@ -3083,6 +3087,7 @@ is_a: OBT:000194 ! animal farm
 [Term]
 id: OBT:000584
 name: dairy starter culture
+synonym: "dairy starter" EXACT []
 is_a: OBT:000432 ! starter culture
 
 [Term]
@@ -3120,8 +3125,8 @@ is_a: OBT:000313 ! host associated biofilm
 
 [Term]
 id: OBT:000591
-name: dental prothesis
-is_a: OBT:000398 ! prothesis
+name: dental prosthesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000592
@@ -3696,7 +3701,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000701
 name: laryngeal prosthetic device
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000702
@@ -3798,11 +3803,13 @@ is_a: OBT:000364 ! organ
 [Term]
 id: OBT:000720
 name: maize feed
+synonym: "corn feed" NARROW []
 is_a: OBT:000229 ! cereal feed
 
 [Term]
 id: OBT:000721
 name: maize storage
+synonym: "corn storage" NARROW []
 is_a: OBT:000423 ! silo
 
 [Term]
@@ -3847,7 +3854,7 @@ is_a: OBT:000341 ! medical outfit
 
 [Term]
 id: OBT:000730
-name: membrane
+name: animal membrane
 is_a: OBT:000196 ! animal tissue
 
 [Term]
@@ -4135,7 +4142,7 @@ is_a: OBT:000371 ! oxidase activity
 [Term]
 id: OBT:000786
 name: pacemaker
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003632 ! prosthetic cardiac device
 
 [Term]
 id: OBT:000787
@@ -4364,7 +4371,8 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000830
 name: prosthetic joint
-is_a: OBT:000398 ! prothesis
+synonym: "joint prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000831
@@ -4988,7 +4996,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000947
 name: veterinary drug
-is_a: OBT:000261 ! drug
+is_a: OBT:003680 ! veterinary product
 
 [Term]
 id: OBT:000948
@@ -6270,6 +6278,7 @@ is_a: OBT:000684 ! industrial equipment
 [Term]
 id: OBT:001190
 name: maize silage
+synonym: "corn silage" NARROW []
 is_a: OBT:000871 ! silage
 
 [Term]
@@ -6334,7 +6343,7 @@ is_a: OBT:000816 ! plant tissue
 [Term]
 id: OBT:001202
 name: mesentery
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001203
@@ -6427,7 +6436,7 @@ is_a: OBT:000710 ! lining
 id: OBT:001219
 name: mucous membrane
 synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001220
@@ -6608,7 +6617,7 @@ is_a: OBT:000642 ! gastrointestinal tract part
 [Term]
 id: OBT:001253
 name: peritoneum
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001254
@@ -7161,6 +7170,7 @@ is_a: OBT:000529 ! broncho-pulmonary segment
 id: OBT:001359
 name: treated wood
 is_a: OBT:000586 ! dead wood
+is_a: OBT:003742 ! wood waste
 
 [Term]
 id: OBT:001360
@@ -7307,7 +7317,7 @@ is_a: OBT:000809 ! pigmented
 [Term]
 id: OBT:001387
 name: yolk sac
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001388
@@ -7600,6 +7610,7 @@ is_a: OBT:001005 ! biofilm phenotype
 [Term]
 id: OBT:001445
 name: birch
+synonym: "birch tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -8108,11 +8119,6 @@ id: OBT:001544
 name: eosinophil
 is_a: OBT:001134 ! granulocyte
 
-[Term]
-id: OBT:001545
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-
 [Term]
 id: OBT:001546
 name: fermented food
@@ -8181,6 +8187,7 @@ is_a: OBT:001097 ! factory
 [Term]
 id: OBT:001558
 name: food processing waste
+synonym: "food residue" RELATED []
 is_a: OBT:001157 ! industrial organic waste
 
 [Term]
@@ -8228,7 +8235,8 @@ is_a: OBT:001114 ! food rind
 [Term]
 id: OBT:001567
 name: fruit tree
-is_a: OBT:001360 ! tree
+comment: horticole meaning
+is_a: OBT:002699 ! cultivated plant
 
 [Term]
 id: OBT:001568
@@ -8740,6 +8748,7 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 [Term]
 id: OBT:001666
 name: oak
+synonym: "oak tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -8999,7 +9008,7 @@ is_a: OBT:001257 ! plankton
 [Term]
 id: OBT:001715
 name: pine forest
-is_a: OBT:001119 ! forest
+is_a: OBT:003881 ! conifer forest
 
 [Term]
 id: OBT:001716
@@ -9013,8 +9022,9 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 
 [Term]
 id: OBT:001718
-name: plant residue
-is_a: OBT:001258 ! plant material
+name: agricultural plant residue
+synonym: "agricultural plant waste" NARROW []
+is_a: OBT:000478 ! agricultural waste
 
 [Term]
 id: OBT:001719
@@ -9043,7 +9053,7 @@ is_a: OBT:001132 ! grain and primary derivative thereof
 
 [Term]
 id: OBT:001724
-name: potato
+name: potato plant
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -9458,8 +9468,8 @@ is_a: OBT:001045 ! confectionery
 
 [Term]
 id: OBT:001803
-name: sugar-beet
-synonym: "betroot" EXACT [TyDI:49625]
+name: sugar-beet plant
+synonym: "betroot plant" EXACT [TyDI:49625]
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -9536,7 +9546,8 @@ is_a: OBT:001159 ! industrial sludge
 
 [Term]
 id: OBT:001818
-name: textile industry
+name: textile mill
+synonym: "textile factory" NARROW []
 is_a: OBT:001097 ! factory
 
 [Term]
@@ -10394,8 +10405,9 @@ is_a: OBT:001621 ! livestock barn
 
 [Term]
 id: OBT:001988
-name: dairy industry
-synonym: "milk industry" RELATED [TyDI:55159]
+name: dairy processing plant
+synonym: "dairy factory" EXACT []
+synonym: "milk processing factory" RELATED [TyDI:55159]
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -10666,7 +10678,7 @@ is_a: OBT:001446 ! bird
 
 [Term]
 id: OBT:002039
-name: food fermentation industry
+name: food fermentation factory
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -10846,7 +10858,7 @@ is_a: OBT:001821 ! tick
 [Term]
 id: OBT:002073
 name: hay
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002074
@@ -10914,7 +10926,7 @@ is_a: OBT:001557 ! food processing factory
 id: OBT:002086
 name: industrial bakery
 synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:003759 ! bakery
 
 [Term]
 id: OBT:002087
@@ -11131,7 +11143,7 @@ is_a: OBT:001802 ! sugar confectionery
 
 [Term]
 id: OBT:002129
-name: meat industry
+name: meat processing plant
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -11442,7 +11454,7 @@ is_a: OBT:001717 ! pistachio and primary derivative thereof
 [Term]
 id: OBT:002190
 name: plant cutting
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002191
@@ -11622,7 +11634,7 @@ is_a: OBT:001744 ! rice based dish
 [Term]
 id: OBT:002225
 name: rice-plant residue
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002226
@@ -11757,7 +11769,7 @@ id: OBT:002251
 name: slaughter plant
 synonym: "abattoir" RELATED [TyDI:50262]
 synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:002129 ! meat processing plant
 
 [Term]
 id: OBT:002252
@@ -11864,7 +11876,7 @@ is_a: OBT:001556 ! food fermentation equipment
 [Term]
 id: OBT:002271
 name: straw
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002272
@@ -12400,7 +12412,7 @@ is_a: OBT:002018 ! environmental water with chemical property
 [Term]
 id: OBT:002372
 name: brewery
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:002373
@@ -12622,7 +12634,7 @@ is_a: OBT:002174 ! pastry product
 [Term]
 id: OBT:002414
 name: creamery
-is_a: OBT:001988 ! dairy industry
+is_a: OBT:001988 ! dairy processing plant
 
 [Term]
 id: OBT:002415
@@ -13150,6 +13162,7 @@ is_a: OBT:002126 ! marine fish meat
 [Term]
 id: OBT:002513
 name: maize
+synonym: "corn" NARROW []
 is_a: OBT:002120 ! maize and primary derivative thereof
 
 [Term]
@@ -14639,7 +14652,7 @@ name: endothelium
 synonym: "endothelial" RELATED [TyDI:52445]
 synonym: "vascular endothelium" EXACT [TyDI:52444]
 is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:002790
@@ -15335,6 +15348,7 @@ is_a: OBT:000710 ! lining
 [Term]
 id: OBT:002914
 name: maize plant
+synonym: "corn plant" NARROW []
 is_a: OBT:002771 ! cereal crop
 
 [Term]
@@ -15752,6 +15766,7 @@ name: hotspring
 synonym: "hot spring" EXACT [TyDI:49581]
 is_a: OBT:000625 ! extreme high temperature environment
 is_a: OBT:001333 ! spring
+is_a: OBT:002019 ! environmental water with physical property
 
 [Term]
 id: OBT:002991
@@ -16371,7 +16386,7 @@ is_a: OBT:001632 ! market garden plant
 
 [Term]
 id: OBT:003098
-name: gum margin
+name: gingival margin
 is_a: OBT:003055 ! gum tissue
 
 [Term]
@@ -17073,7 +17088,7 @@ id: OBT:003221
 name: peritrophic membrane
 is_a: OBT:000200 ! arthropod part
 is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:003222
@@ -17250,8 +17265,8 @@ is_a: OBT:002055 ! fungi as food
 [Term]
 id: OBT:003251
 name: cheese factory
-is_a: OBT:001988 ! dairy industry
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:001988 ! dairy processing plant
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:003252
@@ -17337,6 +17352,7 @@ is_a: OBT:003203 ! heavy metal contaminated soil
 id: OBT:003266
 name: mine waste water
 synonym: "mine wastewater" EXACT [TyDI:51583]
+synonym: "mine water" EXACT []
 is_a: OBT:001212 ! mine waste
 is_a: OBT:002754 ! waste water
 
@@ -18538,7 +18554,7 @@ is_a: OBT:003458 ! semi soft cheese
 
 [Term]
 id: OBT:003475
-name: Granular
+name: Granular cheese
 is_a: OBT:003450 ! hard cheese
 
 [Term]
@@ -19246,3 +19262,3568 @@ synonym: "tejuíno" EXACT [TyDI:51685]
 is_a: OBT:003410 ! corn beverage
 is_a: OBT:003596 ! fermented juice
 
+[Term]
+id: OBT:003602
+name: airway epithelium
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003603
+name: chicken breast meat
+is_a: OBT:002394 ! chicken meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003604
+name: turkey breast meat
+is_a: OBT:002631 ! turkey meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003605
+name: rice bran
+is_a: OBT:001458 ! bran
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003606
+name: lacrimal sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003607
+name: conjunctival sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003608
+name: aneurysmal sac
+synonym: "aneurysm sac" EXACT []
+synonym: "aortic sac" EXACT []
+is_a: OBT:000231 ! circulatory system part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003609
+name: abdominal air sac
+synonym: "air sac" EXACT []
+synonym: "thoracic air sac" EXACT []
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003610
+name: hernial sac
+is_a: OBT:000039 ! animal part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003611
+name: umbilical cord
+is_a: OBT:000463 ! urogenital tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003612
+name: umbilical cord blood
+is_a: OBT:000521 ! blood
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003613
+name: vocal cord
+is_a: OBT:000529 ! broncho-pulmonary segment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003614
+name: cord-shaped
+is_a: OBT:000386 ! phenotype wrt shape
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003615
+name: box lunch
+is_a: OBT:000788 ! packed lunch
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003617
+name: environmental surface
+is_a: OBT:000006 ! artificial environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003618
+name: ceramic tile
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003619
+name: ceramic wall tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003620
+name: ceramic roofing tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003621
+name: stainless steel surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003622
+name: PCV surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003623
+name: plasticized PVC
+synonym: "PVC plastic" NARROW []
+is_a: OBT:003622 ! PCV surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003624
+name: PVC film
+is_a: OBT:000787 ! packaging
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003625
+name: sealed concrete
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003626
+name: bamboo cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003627
+name: wood Cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003628
+name: plastic cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003629
+name: voice prosthesis
+is_a: OBT:003630 ! tracheoesophageal prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003630
+name: tracheoesophageal prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003631
+name: silicone rubber voice prosthesis
+is_a: OBT:003629 ! voice prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003632
+name: prosthetic cardiac device
+synonym: "intracardiac prosthesis" NARROW []
+synonym: "prosthetic cardiovascular device" NARROW []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003633
+name: prosthetic heart valve
+synonym: "heart valve prosthesis" NARROW []
+synonym: "prosthetic valve" NARROW []
+synonym: "valvular prosthesis" NARROW []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003634
+name: mitral valve prosthesis
+synonym: "mitral prosthesis" EXACT []
+is_a: OBT:003633 ! prosthetic heart valve
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003635
+name: aortic prosthetic valve
+synonym: "aortic valve prosthesis" EXACT []
+synonym: "arterial prosthesis" EXACT []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003636
+name: orthopedic prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003637
+name: othopedic implant
+is_a: OBT:003636 ! orthopedic prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003638
+name: hip prosthesis
+synonym: "prosthetic hip joint" EXACT []
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003639
+name: femoral prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003640
+name: knee prosthesis
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003641
+name: shoulder prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003642
+name: cranial prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003643
+name: penile prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003644
+name: testicular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003645
+name: ocular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003646
+name: prosthetic eye
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003647
+name: iris prosthesis
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003648
+name: orbital implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003649
+name: cochlear implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003650
+name: dental implant
+is_a: OBT:000591 ! dental prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003651
+name: palatal obturator prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003652
+name: breast prosthesis
+synonym: "mammary prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003653
+name: breast implant
+is_a: OBT:003652 ! breast prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003654
+name: suction-socket prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003655
+name: granular sludge
+is_a: OBT:001523 ! digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003656
+name: aerobic granular sludge
+is_a: OBT:001861 ! anaerobic digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003657
+name: aerobic granular sludge reactor
+synonym: "AGS reactor" EXACT []
+is_a: OBT:000180 ! aerobic bioreactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003658
+name: granular sludge bed reactor
+synonym: "EGSB reactor" EXACT []
+is_a: OBT:000488 ! anaerobic sludge blanket reactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003659
+name: public swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003660
+name: indoor swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003661
+name: shower bath
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003662
+name: public bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003663
+name: traditional public bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003664
+name: bath basin
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003665
+name: thermal bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003666
+name: thermal saline bath
+is_a: OBT:002592 ! saline water
+is_a: OBT:003665 ! thermal bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003667
+name: mineral bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003668
+name: spa bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003669
+name: seawater bath
+is_a: OBT:003105 ! marine water
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003670
+name: freshwater bath
+is_a: OBT:002455 ! freshwater
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003671
+name: open air bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003672
+name: spring bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003673
+name: hot water bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003674
+name: hot spring bath
+is_a: OBT:002990 ! hotspring
+is_a: OBT:003673 ! hot water bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003675
+name: hot spring spa bath
+is_a: OBT:003674 ! hot spring bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003676
+name: bath sponge
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003677
+name: bath tub heating
+is_a: OBT:000671 ! home heating system
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003678
+name: antiseptic bath
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003679
+name: chlorhexidine bath
+is_a: OBT:003678 ! antiseptic bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003680
+name: veterinary product
+is_a: OBT:000011 ! medical environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003681
+name: insecticide bath
+is_a: OBT:003680 ! veterinary product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003682
+name: antiseptic shower
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003683
+name: dyeing bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003684
+name: skin tannery bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003685
+name: bleach bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003689
+name: mango tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003690
+name: lemon tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003691
+name: peach tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003692
+name: apricot tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003693
+name: quince tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003694
+name: cherry tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003695
+name: khaki tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003696
+name: lime tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003697
+name: carrot plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003698
+name: broccoli plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003699
+name: brussel sprout plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003700
+name: chinese cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003701
+name: collard green plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003702
+name: head cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003703
+name: shallot plant
+is_a: OBT:001389 ! Allium
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003704
+name: fruiting vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003705
+name: courgette plant
+synonym: "zucchini plant" EXACT []
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003706
+name: cucumber plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003707
+name: gherkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003708
+name: melon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003709
+name: pumpkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003710
+name: sweet pepper plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003711
+name: watermelon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003712
+name: leafy vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003713
+name: celery plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003714
+name: spinach plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003715
+name: table water
+is_a: OBT:001530 ! drinking water
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003716
+name: garment factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003717
+name: dyeing factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003718
+name: traditional Chinese fermented cabbage
+is_a: OBT:002321 ! Chinese cabbage
+is_a: OBT:003096 ! fermented vegetable product
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003719
+name: nasal swab
+is_a: OBT:001228 ! nasal secretion
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003720
+name: rum factory
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003721
+name: whisky distillery
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003722
+name: liquor
+is_a: OBT:001397 ! alcoholic drink
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003723
+name: udder
+is_a: OBT:000723 ! mammalian part
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003724
+name: lactic starter
+is_a: OBT:000584 ! dairy starter culture
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003726
+name: plant residue from food processing
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003727
+name: grape pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003728
+name: apple pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003729
+name: olive pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003730
+name: grape must
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003731
+name: sugarcane bagasse
+synonym: "sugar cane bagasse" EXACT []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003732
+name: agave bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003733
+name: citrus bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003734
+name: soy bran
+is_a: OBT:000038 ! animal feed
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003735
+name: palm kernel press cake
+synonym: "residue from palm oil extraction" NARROW []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003736
+name: sugar beet pressed pulp
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003737
+name: cranberry press cake
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003738
+name: forage residue
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003739
+name: cotton plant waste
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003740
+name: cottonseed hull
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003741
+name: olive press cake
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003742
+name: wood waste
+is_a: OBT:000467 ! waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003743
+name: sawdust
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003744
+name: waste house wood
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003745
+name: construction wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003746
+name: demolition wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003747
+name: hazardous industrial waste
+is_a: OBT:000685 ! industrial waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003748
+name: agricultural woody waste
+is_a: OBT:000478 ! agricultural waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003749
+name: wood waste fiber
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003750
+name: transport structure
+is_a: OBT:000162 ! transport equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003751
+name: pallet
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003752
+name: shipping container
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003753
+name: wooden pallet
+is_a: OBT:003751 ! pallet
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003756
+name: wood barrel
+is_a: OBT:000434 ! storage equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003757
+name: oak barrel
+is_a: OBT:003756 ! wood barrel
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003759
+name: bakery
+is_a: OBT:001557 ! food processing factory
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003760
+name: traditional bakery
+is_a: OBT:003759 ! bakery
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003761
+name: traditional dairy
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003762
+name: dairy farm
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003763
+name: snowpack
+is_a: OBT:000881 ! snow
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003764
+name: conifer needle
+is_a: OBT:000807 ! phylloplane part
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003765
+name: agricultural fence
+is_a: OBT:001183 ! livestock habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003766
+name: ungulate
+is_a: OBT:002078 ! herbivore
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003767
+name: biome type forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003768
+name: alpine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003769
+name: tropical rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003770
+name: arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003771
+name: boreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003772
+name: coastal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003773
+name: cooler rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003774
+name: dune forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003775
+name: equatorial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003776
+name: montane forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003777
+name: hemiboreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003778
+name: high altitude forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003779
+name: humid lakeland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003780
+name: low mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003781
+name: subtropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003782
+name: taiga forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003783
+name: lowland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003784
+name: marshy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003785
+name: mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003786
+name: neotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003787
+name: paleotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003788
+name: savannah - forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003789
+name: subalpine forest
+synonym: "sub-alpine forest" EXACT []
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003790
+name: sub-Antarctic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003791
+name: warm sub-tropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003792
+name: dry forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003793
+name: semi - arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003794
+name: semiarid temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003795
+name: hill forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003796
+name: hot forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003797
+name: humid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003798
+name: inland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003799
+name: moist forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003800
+name: plain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003801
+name: pluvial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003802
+name: riverbank forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003803
+name: riverine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003804
+name: submerged forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003805
+name: temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003806
+name: underwater forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003807
+name: upland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003808
+name: volcanic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003809
+name: warm - temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003810
+name: wet forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003811
+name: wildland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003812
+name: drained forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003813
+name: soddy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003814
+name: natural and managed forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003815
+name: natural forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003816
+name: virgin forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003817
+name: uncontrolled forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003818
+name: undisturbed forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003819
+name: unmanaged forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003820
+name: unpolluted forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003821
+name: preserved forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003822
+name: protected forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003823
+name: native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003824
+name: intact forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003825
+name: primary forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003826
+name: primeval forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003827
+name: pristine area of native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003828
+name: pristine forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003829
+name: non-burnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003830
+name: unburnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003831
+name: managed forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003832
+name: man - made forest system
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003833
+name: municipal forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003834
+name: park forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003836
+name: periurban forest
+synonym: "peri-urban" EXACT []
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003837
+name: plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003838
+name: recreational forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003839
+name: reserve forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003840
+name: rural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003841
+name: semi-natural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003842
+name: suburban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003843
+name: urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003844
+name: village-adjacent forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003845
+name: village forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003846
+name: wood forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003847
+name: second-growth forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003848
+name: secondary forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003849
+name: early successional forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003850
+name: burnt forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003851
+name: artificial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003852
+name: commercial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003853
+name: commercial plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003854
+name: community forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003855
+name: disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003856
+name: disturbed urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003857
+name: historical forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003858
+name: human disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003859
+name: old forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003860
+name: mature forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003861
+name: mature forest of high conservation value
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003862
+name: mature old-growth forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003863
+name: young forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003864
+name: forest of given species
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003865
+name: alder forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003866
+name: angiosperm-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003867
+name: arboreal forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003868
+name: argan forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003869
+name: aspen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003870
+name: beach forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003871
+name: beech forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003872
+name: beech-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003873
+name: birch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003874
+name: boreonemoral forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003875
+name: bosque forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003876
+name: broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003877
+name: broadleaf forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003878
+name: Cercocarpus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003879
+name: chestnut forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003880
+name: cloud forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003881
+name: conifer forest
+synonym: "coniferous forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003883
+name: coppice forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003884
+name: cypress forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003885
+name: deciduous forest
+synonym: "deciduous specie forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: deciduous dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: herb-rich coniferous forest
+is_a: OBT:003881 ! conifer forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: evergreen broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: forest with dominant vegetation
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: hardwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: holm-oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
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+name: kelp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003898
+name: larch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003899
+name: lucidophyllous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003900
+name: mangrove forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003901
+name: maple forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003902
+name: maso bamboo forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003903
+name: hemlock fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003904
+name: amabilis fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003906
+name: monodominant forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003907
+name: monospecific forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003908
+name: spruce forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003909
+name: Nothofagaceae forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003910
+name: Nothofagus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003911
+name: oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003912
+name: oak-hickory forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003914
+name: ombrophilous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003916
+name: papyrifera forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003917
+name: perennial forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003918
+name: riparian forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003919
+name: pure forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003920
+name: red pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003921
+name: redwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003922
+name: riparian woodland
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003923
+name: poplar forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003924
+name: sclerophyll forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003925
+name: seasonal dry tropical forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003926
+name: scrub forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003927
+name: semi-evergreen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003928
+name: semideciduous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003929
+name: stone pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003931
+name: tanoak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003932
+name: xeric forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003933
+name: xerophytic forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003934
+name: mix forest
+synonym: "mixed forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003935
+name: papilionoid legume tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003936
+name: leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003937
+name: tulip tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003938
+name: tea-oil tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003939
+name: tea plant
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003940
+name: Syzygiumcordatum tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003941
+name: shea butter tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003942
+name: rubber tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003943
+name: riparian tree specie
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003944
+name: Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003945
+name: Prosopis tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003946
+name: peepal tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003947
+name: Pandanus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003948
+name: pacara earpod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003949
+name: Olea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003950
+name: Nothofagus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003951
+name: mopane tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003952
+name: Masson pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003953
+name: manuka tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003954
+name: loquat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003955
+name: lodgepole pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003956
+name: lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003957
+name: Katsura tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003958
+name: kassod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003959
+name: Hippophae tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003960
+name: dipterocarp tree
+synonym: "Dipterocarpaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003961
+name: Dekopon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003962
+name: cycad tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003963
+name: cupuassu tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003964
+name: cupressaceous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003965
+name: chitalpa tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003966
+name: chinquapin tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003967
+name: Casuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003968
+name: Ascomycota tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003969
+name: Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003970
+name: Allocasuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003971
+name: South-African Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003972
+name: African leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003973
+name: willow tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003974
+name: wild tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003976
+name: whitebark pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003977
+name: White spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003978
+name: white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003979
+name: white oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003980
+name: walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003981
+name: urban tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003982
+name: Ulmus nigra tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003983
+name: Ulmus Dodoens Elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003984
+name: turkey oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003985
+name: tung tree
+synonym: "tung oil tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003986
+name: tanoak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003987
+name: Talh tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003988
+name: sycamore tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003989
+name: sweet chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003990
+name: Swedish spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003991
+name: sudden oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003992
+name: stone pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003993
+name: silver birch
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003994
+name: silk oak
+synonym: "silk oak tree" EXACT []
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003995
+name: Sebertia acuminata
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003996
+name: scot pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003997
+name: riparian Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003998
+name: Rhodococcus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003999
+name: redwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004001
+name: radiata pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004002
+name: Quercus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004003
+name: pygmy tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004004
+name: prunus tree
+synonym: "Prunus spp. tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004005
+name: poplar tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004006
+name: ponderosa pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004007
+name: pomegranate tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004008
+name: pome tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004009
+name: poison oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004010
+name: pistachio tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004011
+name: pinyon pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004012
+name: persimmon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004013
+name: persian walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004014
+name: pepper tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004015
+name: pecan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004016
+name: Paulownia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004017
+name: palm tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004018
+name: ornamental tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004019
+name: ornamental Prunus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004020
+name: orchard tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004021
+name: Gingko tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004022
+name: nutmeg tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004023
+name: nutgall tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004024
+name: norway spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004025
+name: North American white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004026
+name: North American oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004027
+name: needled white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004028
+name: needle pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004029
+name: Monterey pine
+synonym: "insignis pine" EXACT []
+synonym: "radiata pine" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004030
+name: Mongolian pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004031
+name: medlar tree
+synonym: "Mespilus germanica" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004032
+name: Mediterranean oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004033
+name: Maritime pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004034
+name: mangrove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004035
+name: litchi tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004036
+name: laurel tree
+synonym: "Lauraceae tree" EXACT []
+synonym: "lauraceous tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004037
+name: Larix sibirica tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004038
+name: larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004039
+name: kraft pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004040
+name: Korean native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004041
+name: Korean lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004042
+name: Korean fir tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004043
+name: Korea spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004044
+name: kiwifruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004045
+name: khat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004046
+name: jujube tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004047
+name: Juglandaceae walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004048
+name: Japanese Yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004049
+name: Japanese larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004050
+name: jack pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004051
+name: Indian yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004052
+name: Indian oak tree
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004053
+name: Indian cork tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004054
+name: Iberian oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004055
+name: holm oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004056
+name: Himalayan pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004057
+name: hazelnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004058
+name: guava tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004059
+name: grapefruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004060
+name: Garry oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004061
+name: Garcinia schomdurgkiana Pierre tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004062
+name: evergreen oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004063
+name: European white elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004064
+name: European hackberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004065
+name: European elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004066
+name: eucalyptus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004067
+name: English oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004068
+name: Engelmann spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004069
+name: Emory oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004070
+name: Eastern cottonwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004071
+name: Dutch elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004072
+name: deciduous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004073
+name: cypress tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004074
+name: cotton tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004075
+name: Azerbaijani almond tree
+is_a: OBT:001402 ! almond tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004076
+name: coffee tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004077
+name: coconut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004078
+name: cocoa tree
+synonym: "chocolate tree" EXACT []
+synonym: "Theobroma cacao" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004079
+name: clove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004080
+name: clementine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004081
+name: chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004082
+name: Cherry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004083
+name: carob tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004084
+name: camellia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004085
+name: brazil nut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004086
+name: blueberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004087
+name: black oak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004088
+name: Bishop pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004090
+name: Betula tree
+synonym: "Betulaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004091
+name: Betula pendula tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004092
+name: beech tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004093
+name: banyan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004094
+name: avocado tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004095
+name: Austrian pine
+synonym: "Austrian pine tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004096
+name: Australian native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004097
+name: Australian native Grey Box tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004098
+name: Australian Hibiscus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004099
+name: Aspen tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004100
+name: argan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004101
+name: Alep pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004102
+name: ald tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004103
+name: acerola tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004104
+name: acacia tree
+synonym: "acacia" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004106
+name: orchad
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004107
+name: planthopper
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004108
+name: jumping plant lice
+synonym: "Psyllidae" NARROW []
+synonym: "psyllids" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004109
+name: sap-feeding insect
+synonym: "sap-sucking insect" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004110
+name: sentinel plant
+is_a: OBT:000912 ! terrestrial plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004111
+name: peony
+is_a: OBT:004110 ! sentinel plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004112
+name: piercing-sucking insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004113
+name: Myzus persicae
+synonym: "green peach aphid" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004114
+name: cabbage aphid
+synonym: "Brevicoryne brassicae" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004115
+name: phytophagous insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004116
+name: cotton boll worm
+synonym: "Helicoverpa armigera" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004117
+name: black cut worm
+synonym: "Agrotis ipsilon" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004118
+name: cotton leaf worm
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004119
+name: rice yellow stem borer
+synonym: "Scirpophaga incertulas" EXACT []
+is_a: OBT:001652 ! moth
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004120
+name: Asian citrus psyllid
+synonym: "Diaphorina citri" EXACT []
+is_a: OBT:004108 ! jumping plant lice
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004121
+name: vineyard
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004122
+name: Graphocephala versuta
+is_a: OBT:002248 ! sharpshooter
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004123
+name: xylem sap-feeding insect
+is_a: OBT:004109 ! sap-feeding insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:009115
+name: palm forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
-- 
GitLab


From 5189a676bcd517f0825e065247151b51286cf787 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Tue, 12 Jan 2021 16:49:21 +0100
Subject: [PATCH 31/64] evaluation against BioNLP-OST 2019 BB using
 entities.plan

---
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 create mode 100644 process-evaluate_BioNLP-OST.snakefile

diff --git a/.gitignore b/.gitignore
index a788b67c..09e7e901 100644
--- a/.gitignore
+++ b/.gitignore
@@ -42,6 +42,9 @@ corpora/microbes-2019/batch/*/uses.txt
 corpora/microbes-2019/batch/*/words.txt
 corpora/microbes-2019/batch/*/yatea-var/
 corpora/microbes-2019/batch/*/yatea/
+corpora/microbes-2019/expander/
+corpora/microbes-2019/*.full.txt
+corpora/microbes-2019/index/
 .snakemake/
 ancillaries/BioNLP-OST+EnovFood-Habitat.json
 ancillaries/BioNLP-OST+EnovFood-Habitat.paths
diff --git a/config/config.yaml b/config/config.yaml
index f76cb312..9b2c74a1 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -38,6 +38,9 @@ PUBMED_BATCHES_HOME : "corpora/microbes-2019/batch"
 PUBMED_HABITAT_RESULT : "ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt"
 PUBMED_PHENOTYPE_RESULT : "ancillaries/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
 
+## bionlp-ost
+BIONLPOST_BATCHES_HOME : "corpora/BioNLP-OST-2019/batch"
+BIONLPOST_API : "http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/api"
 
 ## index
 ALVISIR_INDEX : "corpora/microbes-2019/index"
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-kb+ner/bionlp-st/BB-kb+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-norm+ner/bionlp-st/BB-norm+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/batch.xml b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/batch.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1
new file mode 100644
index 00000000..4cf00ba2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.a1
@@ -0,0 +1,2 @@
+T1	Title 0 98	Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+T2	Paragraph 99 1053	The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt
new file mode 100644
index 00000000..8eaf96b5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10618167.txt
@@ -0,0 +1,3 @@
+Listeria monocytogenes ActA protein interacts with phosphatidylinositol 4,5-bisphosphate in vitro.
+The N-terminal region of the Listeria monocytogenes ActA protein, in conjunction with host cell factors, is sufficient for actin polymerization at the bacterial surface. Previous data suggested that ActA could protect barbed ends from capping proteins. We tested this hypothesis by actin polymerization experiments in the presence of the ActA N-terminal fragment and capping protein. ActA does not protect barbed ends from capping protein. In contrast, this polypeptide prevents PIP(2) from inhibiting the capping activity of capping protein. Gel filtration and tryptophan fluorescence experiments showed that the purified ActA N-terminal fragment binds to PIP(2) and PIP, defining phosphoinositides as novels ligands for this functional domain of ActA. Phosphoinositide binding to the N-terminal region of ActA may induce conformational changes in ActA and/or facilitate binding of other cell components, important for ActA-induced actin polymerization.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1
new file mode 100644
index 00000000..9b16e214
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.a1
@@ -0,0 +1,6 @@
+T1	Title 0 91	Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+T2	Paragraph 92 228	Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+T3	Paragraph 229 323	To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+T4	Paragraph 324 599	Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+T5	Paragraph 600 1160	Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+T6	Paragraph 1161 1558	Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt
new file mode 100644
index 00000000..f2aba839
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10645449.txt
@@ -0,0 +1,7 @@
+Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru.
+Twenty-nine epidemiological unrelated and mostly multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.
+To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.
+Antimicrobial agent susceptibility testing, major genetic group designation, IS6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA, and pncA genes with mutations commonly associated with drug resistance.
+Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations in pncA.
+Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1
new file mode 100644
index 00000000..2745985f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.a1
@@ -0,0 +1,2 @@
+T1	Title 0 198	Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+T2	Paragraph 199 2107	Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt
new file mode 100644
index 00000000..42e36c58
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10656819.txt
@@ -0,0 +1,3 @@
+Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.
+Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1
new file mode 100644
index 00000000..4a1d8026
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.a1
@@ -0,0 +1,2 @@
+T1	Title 0 134	Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+T2	Paragraph 135 1193	An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt
new file mode 100644
index 00000000..33c13736
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10665543.txt
@@ -0,0 +1,3 @@
+Evaluation of three Brucella soluble antigens used in an indirect Elisa to discriminate S19 vaccinated from naturally infected cattle.
+An O-polysaccharide (O-chain) and a hot-water extracted polysaccharide (PS), both obtained from Brucella abortus 1119-3, and a B. melitensis 16M native hapten (NH) were evaluated by indirect enzyme linked immunosorbent assay (ELISA) on three groups of cattle sera. The sera tested were: (a) 75 sera from cows naturally infected with B. abortus; (b) 130 sera from non-infected and non-vaccinated cattle; and (c) 61 sera from non-infected heifers recently vaccinated with B. abortus Strain 19 (S19). Sensitivity (Se), specificity (Sp) and the capability to discriminate vaccinated cattle (ADV) were determined. Using PS antigen, Se was 100% and the Sp was 97.7%, while the highest Sp was obtained by using the O-chain (99.2% ). For the NH antigen, Se was 94.7% and the Sp was 90.0%. The ADV of the three antigens was approximately 85%. Statistical analysis showed significant differences between O-chain/PS and O-chain/NH antigens. The agreement among antigens determined by kappa coefficient was 0.899 for O-chain/PS, 0.845 for O-chain/NH and 0.795 for PS/NH.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1
new file mode 100644
index 00000000..69691d15
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.a1
@@ -0,0 +1,2 @@
+T1	Title 0 65	Immune response to infection with Salmonella typhimurium in mice.
+T2	Paragraph 66 1103	Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt
new file mode 100644
index 00000000..83aafb4f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10770276.txt
@@ -0,0 +1,3 @@
+Immune response to infection with Salmonella typhimurium in mice.
+Infection of mice with Salmonella typhimurium results in systemic infection and a disease similar to that seen in humans after infection with S. typhi. The innate immune system can restrict replication of S. typhimurium to a certain degree, but for effective control and eradication of bacteria, acquired immunity is essential. Salmonella infection induces the generation of specific CD4+ and CD8+ T cells, and both T cell populations are important for protection during primary and secondary responses, although the mechanisms underlying T cell-mediated protection are not yet completely understood. Infection with S. typhimurium also results in a strong antibody response to Salmonella antigens and, in contrast to most other intracellular bacteria, this antibody response participates in protection. In summary, the response to S. typhimurium involves both T and B cell-mediated immunity, and mechanisms mediated by both lymphocyte populations are important for control of primary infection and protection against secondary infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1
new file mode 100644
index 00000000..a70f957b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.a1
@@ -0,0 +1,2 @@
+T1	Title 0 139	The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+T2	Paragraph 140 1995	Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt
new file mode 100644
index 00000000..65ac1b5c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10792385.txt
@@ -0,0 +1,3 @@
+The role of Fcgamma receptor polymorphisms and C3 in the immune defence against Neisseria meningitidis in complement-deficient individuals.
+Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1
new file mode 100644
index 00000000..302a2caf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+T2	Paragraph 81 1417	Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt
new file mode 100644
index 00000000..6d702a90
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-10796014.txt
@@ -0,0 +1,3 @@
+Symbiotic induction of pyruvate dehydrogenase genes from Sinorhizobium meliloti.
+Genes coding for components of the pyruvate dehydrogenase (PDH) multienzyme complex (PDHc) from Sinorhizobium meliloti, the alfalfa symbiont, have been isolated on the basis of their high expression in symbiotic bacteria. The Elp component, PDH, is encoded by two genes, pdhAalpha (1,047 bp) and pdhAbeta (1,383 bp), a situation encountered in the alpha-proteobacteria Rickettsia prowazekii and Zymomonas mobilis as well as in some gram-positive bacteria and in mitochondria. pdhAalpha and pdhAbeta precede pdhB (1,344 bp), which encodes the E2p component, dihydrolipoamide acetyltransferase, of the PDHc. No gene encoding the E3 component, lipoamide dehydrogenase, was found in the immediate vicinity of pdhA and pdhB genes. pdhAalpha, pdhAbeta and pdhB likely constitute an operon. Here, we provide evidence that pdhA expression is induced in the symbiotic stage, compared with free-living conditions. We demonstrate that symbiotic expression of pdhA genes does not depend on the fix LJ regulatory cascade that regulates nitrogen fixation and respiration gene expression in symbiotic S. meliloti cells. Induction of pdhA expression could be obtained under free-living conditions upon the addition of pyruvate to the culture medium. Induction by pyruvate and symbiotic activation of pdh gene expression take place at the same promoter.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1
new file mode 100644
index 00000000..57aa6063
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.a1
@@ -0,0 +1,2 @@
+T1	Title 0 75	Cloning and expression analysis of Phytoplasma protein translocation genes.
+T2	Paragraph 76 1369	Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt
new file mode 100644
index 00000000..16fa7366
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-11551069.txt
@@ -0,0 +1,3 @@
+Cloning and expression analysis of Phytoplasma protein translocation genes.
+Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohistochemical thin sections observed by optical microscopy showed that SecA is characteristically present in plant phloem tissues infected with phytoplasma. The secY gene consists of 1,239 nucleotides encoding a 413 amino acid protein (45.9 kDa) and shows the highest similarity with SecY of B. subtilis. These results suggest the presence of a functional Sec system in phytoplasmas. Because phytoplasmas are endocellular bacteria lacking cell walls, this system might secrete bacterial proteins directly into the host cytoplasm. This study is what we believe to be the first report of the sequence and expression analysis of phytoplasma genes encoding membrane proteins with a predicted function.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1
new file mode 100644
index 00000000..bdb60b8e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.a1
@@ -0,0 +1,2 @@
+T1	Title 0 189	Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+T2	Paragraph 190 1564	Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt
new file mode 100644
index 00000000..16b1030e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12417169.txt
@@ -0,0 +1,3 @@
+Emergence of resistance of vancomycin-resistant Enterococcus faecium in a thermal injury patient treated with quinupristin-dalfopristin and cultured epithelial autografts for wound closure.
+Vancomycin-resistant Enterococcus faecium and faecalis (VRE) remains a major complication among critically ill patients. A 26-year-old patient with 65% total body surface area burns (TBSA) was infected with several E. faecium strains during his admission that were resistant to vancomycin. Because chloramphenicol was the standard treatment at this time, this drug was initiated until, the organism was identified as E. faecium and reported as susceptible to quinupristin-dalfopristin. Given these data, it was then decided to discontinue the chloramphenicol therapy. Quinupristin-dalfopristin therapy resulted in initial reduction of fever and white blood cell counts that continued over the next 5 days. However, on day 7 of quinupristin-dalfopristin therapy, a return of fever and elevation of the white blood cell count was noted and a repeated E. faecium blood culture demonstrated sudden resistance to quinupristin-dalfopristin (Bauer-Kirby zone size <14 mm). Chloramphenicol was restarted and the patient improved slowly over a period of 16 days. Our indigenous VRE had limited exposure to quinupristin-dalfopristin in the recent past; however, resistance emerged with the first commercial use of this agent in our burn treatment center. High-dose chloramphenicol treatment did not appear to impair engraftment of cultured epithelial autografts (CEA) in this patient.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1
new file mode 100644
index 00000000..33520a3f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.a1
@@ -0,0 +1,2 @@
+T1	Title 0 130	Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+T2	Paragraph 131 2105	Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt
new file mode 100644
index 00000000..9d4ccf76
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12438382.txt
@@ -0,0 +1,3 @@
+Pathological and therapeutic significance of cellular invasion by Proteus mirabilis in an enterocystoplasty infection stone model.
+Proteus mirabilis infection often leads to stone formation. We evaluated how bacterium-mucin adhesion, invasion, and intracellular crystal formation are related to antibiotic sensitivity and may cause frequent stone formation in enterocystoplasties. Five intestinal (Caco-2, HT29, HT29-18N2, HT29-FU, and HT29-MTX) and one ureter cell line (SV-HUC-1) were incubated in artificial urine with five Proteus mirabilis strains. Fluorescence-activated cell sorting (FACS), laser scanning microscopy, and electron microscopy evaluated cellular adhesion and/or invasion, pathologic changes to mitochondria, and P. mirabilis-mucin colocalization (MUC2 and MUC5AC). An MTT (thiazolyl blue tetrazolium bromide) assay and FACS analysis of caspase-3 evaluated the cellular response. Infected cells were incubated with antibiotics at dosages representing the expected urinary concentrations in a 10-year-old, 30-kg child to evaluate bacterial invasion and survival. All cell lines showed colocalization of P. mirabilis with human colonic mucin (i.e., MUC2) and human gastric mucin (i.e., MUC5AC). The correlation between membrane mucin expression and invasion was significant and opposite for SV-HUC-1 and HT29-MTX. Microscopically, invasion by P. mirabilis with intracellular crystal formation and mitochondrial damage was found. Double membranes surrounded bacteria in intestinal cells. Relative resistance to cotrimoxazole and augmentin was found in the presence of epithelial cells. Ciprofloxacin and gentamicin remained effective. Membrane mucin expression was correlated with relative antibiotic resistance. Cell invasion by P. mirabilis and mucin- and cell type-related distribution and response differences indicate bacterial tropism that affects crystal formation and mucosal presence. Bacterial invasion seems to have cell type-dependent mechanisms and prolong bacterial survival in antibiotic therapy, giving a new target for therapeutic optimalization of antibiotic treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1
new file mode 100644
index 00000000..bcbd5de9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.a1
@@ -0,0 +1,2 @@
+T1	Title 0 120	Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+T2	Paragraph 121 1520	Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt
new file mode 100644
index 00000000..1e61e793
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-12934822.txt
@@ -0,0 +1,3 @@
+Detection of Cryptosporidium parvum in secondary effluents using a most probable number-polymerase chain reaction assay.
+Polymerase chain reaction (PCR) was used to detect Cryptosporidium parvum oocysts in secondary effluent samples collected from activated-sludge facilities. Serial dilutions of the purified nucleic acid extracts from the samples were made and PCR was conducted to estimate the C. parvum oocyst concentration via a Poisson distribution-based most probable number (MPN). The degree of oocysts associated with wastewater particles was also evaluated. The sensitivity of the MPN-PCR assay was 20 oocysts/PCR unit. The detection limit of the concentration, extraction, and purification protocols in phosphate buffer saline spiked with a known concentration of oocysts ranged from 1.1 to 4.6 oocysts/L; the detection limit for the wastewater samples ranged from 11 to 4200 oocysts/L depending on the extent of inhibition in each sample. The recovery efficiency of the oocysts ranged from 48 to 59% in most samples. Oocysts were found in two out of seven samples with concentrations of 203 and 308 oocysts/L, as estimated by the MPN-PCR method. The oocysts were found only in the filtrate of the grab samples; particle-associated oocysts were not detected. Association of spiked C. parvum oocysts with particles in secondary effluent drawn from wastewater plants with varying operating conditions indicated a weak correlation between the degree of association and the mean cell residence time of the system.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1
new file mode 100644
index 00000000..54572651
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.a1
@@ -0,0 +1,2 @@
+T1	Title 0 172	Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+T2	Paragraph 173 1767	We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt
new file mode 100644
index 00000000..6395511a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14638480.txt
@@ -0,0 +1,3 @@
+Efficacies of vancomycin, arbekacin, and gentamicin alone or in combination against methicillin-resistant Staphylococcus aureus in an in vitro infective endocarditis model.
+We adopted an in vitro infective endocarditis model (IVIEM) to compare the efficacy of vancomycin (VAN), arbekacin (ABK), and gentamicin (GEN) alone or in combination. Using two strains of clinically isolated methicillin-resistant Staphylococcus aureus, one GEN susceptible (GS171) and one GEN resistant (GR153), fibrin clots were prepared and suspended in the IVIEM. Antibiotics were given as boluses every 6 h (q6h), q12h, or q24h or by continuous infusion with VAN, q12h or q24h with ABK, and q8h or q24h with GEN. For combination treatment, VAN q12h plus ABK q24h and VAN q12h plus GEN q24h were given. Fibrin clots were removed from each model at 0, 8, 24, 32, 48, and 72 h, and the bacterial densities were determined. The number of colonies within the fibrin clot was significantly decreased in all study groups compared with control groups (P<0.001). When VAN and ABK were administered alone, the number of colonies was significantly lower in GS171 than in GR153 by 8 h after administration (P=0.02) and was lowest in GS171 when ABK was administered q12h (P=0.01). At 72 h, ABK or VAN alone produced equivalent bacterial reductions regardless of dosing frequency and GEN resistance. In GR153, VAN plus ABK showed an additive effect till 24 h, although VAN plus GEN showed indifference. Our data suggest that ABK could be used as an alternative to VAN in GEN-resistant staphylococcal endocarditis. An additive effect was seen when VAN and ABK were used together in GEN-resistant strains until 24 h; however, further studies are warranted for the clinical application of this combination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1
new file mode 100644
index 00000000..8d8e0bc7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.a1
@@ -0,0 +1,2 @@
+T1	Title 0 155	Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+T2	Paragraph 156 718	The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt
new file mode 100644
index 00000000..d75a6b94
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-14657131.txt
@@ -0,0 +1,3 @@
+Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.
+The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1
new file mode 100644
index 00000000..085b1200
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.a1
@@ -0,0 +1,2 @@
+T1	Title 0 148	Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+T2	Paragraph 149 2161	The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt
new file mode 100644
index 00000000..bb01ab19
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15273106.txt
@@ -0,0 +1,3 @@
+Modulation of fibronectin adhesins and other virulence factors in a teicoplanin-resistant derivative of methicillin-resistant Staphylococcus aureus.
+The impact of glycopeptide resistance on the molecular regulation of Staphylococcus aureus virulence and attachment to host tissues is poorly documented. We compared stable teicoplanin-resistant methicillin-resistant S. aureus (MRSA) strain 14-4 with its teicoplanin-susceptible MRSA parent, strain MRGR3, which exhibits a high degree of virulence in a rat model of chronic foreign body MRSA infection. The levels of fibronectin-mediated adhesion and surface display of fibronectin-binding proteins were higher in teicoplanin-resistant strain 14-4 than in its teicoplanin-susceptible parent or a teicoplanin-susceptible revertant (strain 14-4rev) that spontaneously emerged during tissue cage infection. Quantitative reverse transcription-PCR (qRT-PCR) showed four- and twofold higher steady-state levels of fnbA and fnbB transcripts, respectively, in strain 14-4 than in its teicoplanin-susceptible counterparts. Analysis of global regulatory activities by qRT-PCR revealed a strong reduction in the steady-state levels of RNAIII and RNAII in the teicoplanin-resistant strain compared to in its teicoplanin-susceptible counterparts. In contrast, sarA mRNA levels were more than fivefold higher in strain 14-4 than in MRGR3 and 14-4rev. Furthermore, the alternative transcription factor sigma B had a higher level of functional activity in the teicoplanin-resistant strain than in its teicoplanin-susceptible counterparts, as evidenced by significant increases in both the sigma B-dependent asp23 mRNA levels and the sarA P3 promoter-derived transcript levels, as assayed by qRT-PCR and Northern blotting, respectively. These data provide further evidence that the emergence of glycopeptide resistance is linked by still poorly understood molecular pathways with significant pleiotropic changes in the expression and regulation of some major virulence genes. These molecular and phenotypic changes may have a profound impact on the bacterial adhesion and colonization properties of such multiresistant organisms.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1
new file mode 100644
index 00000000..9be12197
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.a1
@@ -0,0 +1,2 @@
+T1	Title 0 39	Mycoplasma otitis in California calves.
+T2	Paragraph 40 1415	A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt
new file mode 100644
index 00000000..d5841102
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15460321.txt
@@ -0,0 +1,3 @@
+Mycoplasma otitis in California calves.
+A retrospective study of Mycoplasma otitis in California calves submitted for necropsy between 1993 and 2002 was conducted to characterize the demographic features of the disease and the pathologic findings associated with infection. Sixty-one confirmed cases of Mycoplasma otitis were identified among 20,525 necropsied cattle. All affected animals were calves, ranging in age from 2 weeks to 4 months and with a median age of 1.5 months. Ninety-two percent of the cases were dairy breeds. A higher percent of necropsied calves with Mycoplasma otitis were males (0.45%) than females (0.23%). The proportion of cases that had Mycoplasma otitis increased from 1993 to 2002, and there was a significant (P < 0.05) seasonal distribution, with the highest proportion in the spring and the lowest in the summer months. Infections involved both the middle and inner ear and were characterized by a suppurative inflammatory response with extensive bony involvement. Three species of Mycoplasma were isolated from the ears: M. bovis, M. bovirhinis, and M. alkalescens. Concurrent pneumonia occurred in 47 cases (77%), and Mycoplasma was isolated from the lungs of 30 of those cases. The increasing proportion of Mycoplasma otitis cases in the past 10 years emphasizes the importance of identifying risk factors that could be modified to lower the incidence of this disease in calves.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1
new file mode 100644
index 00000000..33f615f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.a1
@@ -0,0 +1,5 @@
+T1	Title 0 87	Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+T2	Paragraph 88 438	Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+T3	Paragraph 439 962	The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+T4	Paragraph 963 1906	There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+T5	Paragraph 1907 2082	The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt
new file mode 100644
index 00000000..14a05a0a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15612668.txt
@@ -0,0 +1,6 @@
+Diagnosis of atrophic body gastritis in Chinese patients by measuring serum pepsinogen.
+Atrophic body gastritis (ABG) is common in China. Although histology via endoscopy is an efficient and reliable means of diagnosing ABG, it is an invasive procedure. Therefore, in the present study serum pepsinogen (PG) was used as a biomarker to develop a novel noninvasive test as the first option for screening of ABG in certain groups of Chinese.
+The study population consisted of 81 selected dyspeptic patients (mean age, 64.8 +/- 0.7 years; M:F, 43:38) who underwent diagnostic gastroscopy. At least four biopsy specimens were taken from the antrum and corpus of the stomach (two specimens from each site) for histological diagnosis. Blood samples for ELISA assays of serum pepsinogen I (PGI), pepsinogen II (PGII) and IgG antibodies against Helicobacter pylori (Hp IgG) were drawn after endoscopy. Cut-off points were calculated using receiver operating curves (ROC).
+There was no correlation between serum PG and atrophy in the antral mucosa. The mean serum concentration of PGI was lower (P < 0.05) in patients with ABG (89.9 microg/L) than in those with normal mucosa (NM) and non-ABG (123.7 microg/L and 139.1 microg/L). The mean ratio of PGI:PGII was also lower (P < 0.01) in patients with ABG (6.2) than in those with NM and non-ABG (11.6 and 11.7). There was no difference in serum PGI or the PGI:PGII ratio between patients with and without H. pylori infection. For diagnosing ABG, the area under the ROC of PGI and the PGI:PGII ratio was 0.741 (95% CI: 0.627-0.856) and 0.874 (95% CI: 0.788-0.961), respectively. The maximum of the Youden's index (YI) of PGI and the PGI:PGII ratio was 0.426 and 0.722, respectively. The best cut-off point for PGI was 97.1 microg/L with sensitivity of 67% and specificity of 76%, and for PGI:PGII ratio was 8.1 microg/L, with sensitivity of 89% and specificity of 83%.
+The serum PGI:PGII ratio appears to be a sensitive and specific assay for corpus atrophy, thus providing a noninvasive and indicative test for diagnosis of atrophic gastritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1
new file mode 100644
index 00000000..488cb271
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 69	Haemophilus influenzae: a significant pathogen in acute otitis media.
+T2	Paragraph 70 586	Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt
new file mode 100644
index 00000000..21581337
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-15626953.txt
@@ -0,0 +1,3 @@
+Haemophilus influenzae: a significant pathogen in acute otitis media.
+Haemophilus influenzae is a major pathogen in acute otitis media (AOM) causing disease that is not clinically distinguishable from that caused by Streptococcus pneumoniae. AOM caused by H. influenzae is particularly associated with older age and recurrent disease. Antibiotics differ in their ability to eradicate H. influenzae from the middle ear space. In the United States, widespread pneumococcal vaccination has increased the importance of H. influenzae as a major therapeutic challenge in the treatment of AOM.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1
new file mode 100644
index 00000000..75d3dda7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.a1
@@ -0,0 +1,2 @@
+T1	Title 0 81	[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+T2	Paragraph 82 2086	Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt
new file mode 100644
index 00000000..9fa1251c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-1649682.txt
@@ -0,0 +1,3 @@
+[The use of rifampin in the treatment of infection due to Staphylococcus aureus].
+Infection due to Staphylococcus aureus continues to be a source of significant morbidity and mortality. However, its treatment is increasingly complicated by the rising prevalence of resistance to antibiotics. Apart from the two recognized modes of staphylococcal resistance, namely, penicillinase production and intrinsic resistance, Sabath and associates have described a third type in which resistance is manifested by susceptibility to growth inhibition but tolerance to the lethal action of bactericidal agents. The mechanism of tolerance is attributed to a deficiency of autolytic enzyme activity in the part of bacteria, possibly secondary to an inhibition of autolysins in the tolerant staphylococcal strains. These strains are found in patients with infections responding poorly to treatment with cell-wall active antibiotics including vancomycin. Because of its unique mechanism of action and pharmacokinetic properties, rifampin has been reported to be the most active among 65 antistaphylococcal agents tested and have the capacity to kill intraleukocytic staphylococci. We present 2 cases who were cured following the addition of rifampin to previously established regimens. Case 1 was a 40-year-old male who had fever, cough, dyspnea, a right elbow abscess and left leg swelling for 2 weeks prior to admission. Culture of purulent material from the elbow abscess grew staphylococcus aureus. Chest X-ray showed bilateral septic embolism and phleborheography showed partial deep vein occlusion of the left ileofemoral vein. Case 2 was 22-year-old female with fever, chills and cough for 3 weeks. Blood culture grew staphylococcus aureus, and Chest X-ray revealed bilateral septic embolism with pneumonia. Neither of them responded to standard antibiotics which were judged adequate by in vitro sensitivity tests. Clinical cure was later obtained after rifampin was added to the regimens. These results suggest that rifampin may be a useful adjunct in the therapy of staphylococcal infections.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1
new file mode 100644
index 00000000..6f0152ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.a1
@@ -0,0 +1,2 @@
+T1	Title 0 147	[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+T2	Paragraph 148 1268	Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt
new file mode 100644
index 00000000..f6407964
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16510930.txt
@@ -0,0 +1,3 @@
+[Results of serotyping of strains isolated from patients with ulcerative colitis (colitis gravis), adaptive colitis and chronic catarrhal colitis].
+Serotyping of 565 E.coli strains isolated from 273 patients with ulcerative colitis (70 patients); chronic catarrhal colitis (96 patients), adaptive colitis (107 patient) and of 72 E. coli strains isolated from 50 practically healthy persons (control group) was performed. Serotyping was performed in reaction of agglutination, on stage-glass, by use of commercial set consisting of O and H monovalent serum. As a result of performed investigation it was determined, that in patients with different intestinal inflammatory pathologies, there were found significant pathologic changes in intestinal microbiocenosis, in which main role are playing by strains of E. coli. Such violations of intestinal microbiocenosis often are leading to complications of basic disease. Serotyping of E. coli strains has shown, that in formation of pathologic microbiocenosis with more or less equal frequency are taking part enteropathogenic, enteroinvasive, enterotoxic strains of E. coli and also some definite serotypes of E. coli - representatives of normal intestinal microflora with ability of synthesis of thermolabile enterotoxin.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1
new file mode 100644
index 00000000..5c7196e7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.a1
@@ -0,0 +1,2 @@
+T1	Title 0 138	Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+T2	Paragraph 139 1612	Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt
new file mode 100644
index 00000000..ce7e05c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-16728960.txt
@@ -0,0 +1,3 @@
+Swarming differentiation of vibrio vulnificus downregulates the expression of the vvhBA hemolysin gene via the LuxS quorum-sensing system.
+Swarming has proven to be a good in vitro model for bacterial surface adherence and colonization, and the swarming differentiation of a bacterium has been shown to be coupled with changes in the expression of virulence factors associated with its invasiveness, particularly in the early stages of infection. In this study, we attempted to determine whether the expression of vvhA, which encodes for hemolysin/cytolysin (VvhA), is either upregulated or downregulated during the swarming differentiation of V. vulnificus. The insertional inactivation of vvhA itself exerted no detectable effect on the expression of V. vulnificus swarming motility. However, in our lacZ-fused vvhA transcriptional reporter assay, vvhA expression decreased in swarming V. vulnificus as compared to non-swarming or planktonic V. vulnificus. The reduced expression of vvhA in swarming V. vulnificus increased as a result of the deletional inactivation of luxS, a gene associated with quorum sensing. These results show that vvhA expression in swarming V. vulnificus is downregulated via the activity of the LuxS quorum-sensing system, suggesting that VvhA performs no essential role in the invasiveness of V. vulnificus via the adherence to and colonization on the body surfaces required in the early stages of the infection. However, VvhA may play a significant role in the pathophysiological deterioration occurring after swarming V. vulnificus is differentiated into planktonic V. vulnificus.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1
new file mode 100644
index 00000000..1a8bb7e1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.a1
@@ -0,0 +1,2 @@
+T1	Title 0 165	Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+T2	Paragraph 166 1658	The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt
new file mode 100644
index 00000000..074f19ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-17261513.txt
@@ -0,0 +1,3 @@
+Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis.
+The recent expansion of genetic and genomic tools for metabolic engineering has accelerated the development of microorganisms for the industrial production of desired compounds. We have used transposable elements to identify chromosomal locations in the obligate methanotroph Methylomonas sp. strain 16a that support high-level expression of genes involved in the synthesis of the C(40) carotenoids canthaxanthin and astaxanthin. with three promoterless carotenoid transposons, five chromosomal locations-the fliCS, hsdM, ccp-3, cysH, and nirS regions-were identified. Total carotenoid synthesis increased 10- to 20-fold when the carotenoid gene clusters were inserted at these chromosomal locations compared to when the same carotenoid gene clusters were integrated at neutral locations under the control of the promoter for the gene conferring resistance to chloramphenicol. A chromosomal integration system based on sucrose lethality was used to make targeted gene deletions or site-specific integration of the carotenoid gene cluster into the Methylomonas genome without leaving genetic scars in the chromosome from the antibiotic resistance genes that are present on the integration vector. The genetic approaches described in this work demonstrate how metabolic engineering of microorganisms, including the less-studied environmental isolates, can be greatly enhanced by identifying integration sites within the chromosome of the host that permit optimal expression of the target genes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1
new file mode 100644
index 00000000..e01673de
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.a1
@@ -0,0 +1,2 @@
+T1	Title 0 126	Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+T2	Paragraph 127 1238	Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt
new file mode 100644
index 00000000..1926885a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19494280.txt
@@ -0,0 +1,3 @@
+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1
new file mode 100644
index 00000000..cd59e1a7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.a1
@@ -0,0 +1,2 @@
+T1	Title 0 122	Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+T2	Paragraph 123 1943	Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt
new file mode 100644
index 00000000..f8d5183d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-19656787.txt
@@ -0,0 +1,3 @@
+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1
new file mode 100644
index 00000000..945863c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.a1
@@ -0,0 +1,5 @@
+T1	Title 0 51	Microbiota in pediatric inflammatory bowel disease.
+T2	Paragraph 52 236	To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+T3	Paragraph 237 656	Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+T4	Paragraph 657 1012	Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+T5	Paragraph 1013 1135	The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt
new file mode 100644
index 00000000..649f7bdb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20400104.txt
@@ -0,0 +1,6 @@
+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1
new file mode 100644
index 00000000..24f67c01
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+T2	Paragraph 113 1783	Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt
new file mode 100644
index 00000000..4f4745aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-20672296.txt
@@ -0,0 +1,3 @@
+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1
new file mode 100644
index 00000000..d1507feb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.a1
@@ -0,0 +1,2 @@
+T1	Title 0 123	TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+T2	Paragraph 124 1634	During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt
new file mode 100644
index 00000000..ae4fde14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21148810.txt
@@ -0,0 +1,3 @@
+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1
new file mode 100644
index 00000000..aa66ed99
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.a1
@@ -0,0 +1,2 @@
+T1	Title 0 152	Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+T2	Paragraph 153 2216	Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt
new file mode 100644
index 00000000..3043d3c5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21476570.txt
@@ -0,0 +1,3 @@
+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1
new file mode 100644
index 00000000..3072e386
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.a1
@@ -0,0 +1,2 @@
+T1	Title 0 73	Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+T2	Paragraph 74 1737	The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt
new file mode 100644
index 00000000..40c32e07
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21511409.txt
@@ -0,0 +1,3 @@
+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1
new file mode 100644
index 00000000..1faafc2a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.a1
@@ -0,0 +1,2 @@
+T1	Title 0 52	Insights into Acinetobacter baumannii pathogenicity.
+T2	Paragraph 53 988	Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt
new file mode 100644
index 00000000..ebda2294
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-21989983.txt
@@ -0,0 +1,3 @@
+Insights into Acinetobacter baumannii pathogenicity.
+Acinetobacter spp. have justifiably received significant attention from the public, scientific, and medical communities. Over recent years, Acinetobacter, particularly Acinetobacter baumannii, has become a "red-alert" human pathogen, primarily because of its exceptional ability to develop resistance to all currently available antibiotics. This characteristic is compounded by its unique abilities to survive in a diverse range of environments, including those within healthcare institutions, leading to problematic outbreaks. Historically, the virulence of the organism has been questioned, but recent clinical reports suggest that Acinetobacter can cause serious, life-threatening infections. Furthermore, its metabolic adaptability gives it a selective advantage in harsh hospital environments. This review focuses on current understanding of A. baumannii pathogenesis and the model systems used to study this interesting organism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1
new file mode 100644
index 00000000..c66aefb3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.a1
@@ -0,0 +1,2 @@
+T1	Title 0 118	Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+T2	Paragraph 119 1349	Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt
new file mode 100644
index 00000000..f80656db
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22203552.txt
@@ -0,0 +1,3 @@
+Characterization and screening of plant probiotic traits of bacteria isolated from rice seeds cultivated in Argentina.
+Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1
new file mode 100644
index 00000000..b5d80c02
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 119	Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+T2	Paragraph 120 1548	The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt
new file mode 100644
index 00000000..a5aa4ccb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-22537874.txt
@@ -0,0 +1,3 @@
+Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.
+The Escherichia coli plasmid-encoded urease, a virulence factor in human and animal infections of the urinary and gastroduodenal tracts, is induced when the substrate urea is present in the growth medium. Urea-dependent urease expression is mediated at the transcriptional level by the AraC-like activator UreR. Previous work has shown that a peptide representing the N-terminal 194 amino-acid residues of UreR binds urea at a single site, full-length UreR forms an oligomer, and the oligomerization motif is thought to reside in the N-terminal portion of the molecule. The C-terminal domain of UreR contains two helix-turn-helix motifs presumed to be necessary for DNA binding. In this study, we exploited mutational analyses at the N-terminal domain of UreR to determine if this domain dimerizes similar to other AraC family members. UreR mutants were analyzed for the ability to activate transcription of lacZ from an ureDp-lacZ transcriptional fusion. A construct encoding the N-terminal 194 amino acids of UreR, eluted as an oligomer by gel filtration and had a dominant negative phenotype over the wild-type ureR allele. We hypothesize that this dominant negative phenotype results from the formation of inactive heterodimers between wild-type and truncated UreR. Dominant negative analysis and cross-linking assays demonstrated that E. coli UreR is active as a dimer and dimerization occurs within the first 180 residues.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1
new file mode 100644
index 00000000..bbdc2592
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.a1
@@ -0,0 +1,2 @@
+T1	Title 0 193	Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+T2	Paragraph 194 1519	A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt
new file mode 100644
index 00000000..0dddab5d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-23645023.txt
@@ -0,0 +1,3 @@
+Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus.
+A light-yellow-coloured bacterium, designated strain PTJT-5(T), was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and pH 6.0-7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5(T) was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8(T) (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5(T) is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5(T) ( = CCTCC AB 2013017(T) = KCTC 32316(T)). An emended description of Flavihumibacter petaseus is also proposed. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1
new file mode 100644
index 00000000..7975cca8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.a1
@@ -0,0 +1,2 @@
+T1	Title 0 64	Molecular determinants for a cardiovascular collapse in anthrax.
+T2	Paragraph 65 1197	Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt
new file mode 100644
index 00000000..5971b3f3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24389148.txt
@@ -0,0 +1,3 @@
+Molecular determinants for a cardiovascular collapse in anthrax.
+Bacillus anthracis releases two bipartite proteins, lethal toxin and edema factor, that contribute significantly to the progression of anthrax-associated shock. As blocking the anthrax toxins prevents disease, the toxins are considered the main virulence factors of the bacterium. The anthrax bacterium and the anthrax toxins trigger multi-organ failure associated with enhanced vascular permeability, hemorrhage and cardiac dysfunction in animal challenge models. A recent study using mice that either lacked the anthrax toxin receptor in specific cells and corresponding mice expressing the receptor in specific cell types demonstrated that cardiovascular cells are critical for disease mediated by anthrax lethal toxin. These studies are consistent with involvement of the cardiovascular system, and with an increase of cardiac failure markers observed in human anthrax and in animal models using B. anthracis and anthrax toxins. This review discusses the current state of knowledge regarding the pathophysiology of anthrax and tries to provide a mechanistic model and molecular determinants for the circulatory shock in anthrax. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1
new file mode 100644
index 00000000..ece1a695
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.a1
@@ -0,0 +1,2 @@
+T1	Title 0 80	On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+T2	Paragraph 81 1178	The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt
new file mode 100644
index 00000000..4d5b094e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24584903.txt
@@ -0,0 +1,3 @@
+On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum.
+The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1
new file mode 100644
index 00000000..f838186e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.a1
@@ -0,0 +1,2 @@
+T1	Title 0 117	Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+T2	Paragraph 118 1813	Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt
new file mode 100644
index 00000000..736e7356
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24739626.txt
@@ -0,0 +1,3 @@
+Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
+Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1
new file mode 100644
index 00000000..ca40354a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+T2	Paragraph 134 1870	Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt
new file mode 100644
index 00000000..25d74d4e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24794581.txt
@@ -0,0 +1,3 @@
+The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus).
+Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1
new file mode 100644
index 00000000..6c326bbe
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.a1
@@ -0,0 +1,2 @@
+T1	Title 0 112	Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+T2	Paragraph 113 1156	Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt
new file mode 100644
index 00000000..f95b2bc9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-24865686.txt
@@ -0,0 +1,3 @@
+Mycobacterium tuberculosis isolates from single outpatient clinic in Panama City exhibit wide genetic diversity.
+Understanding Mycobacterium tuberculosis biodiversity and transmission is significant for tuberculosis control. This short report aimed to determine the genetic diversity of M. tuberculosis isolates from an outpatient clinic in Panama City. A total of 62 M. tuberculosis isolates were genotyped by 12 loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and Spoligotyping. Forty-five (72.6%) of the isolates showed unique MIRU-VNTR genotypes, and 13 (21%) of the isolates were grouped into four clusters. Four isolates showed polyclonal MIRU-VNTR genotypes. The MIRU-VNTR Hunter-Gaston discriminatory index reached 0.988. The Spoligotyping analysis revealed 16 M. tuberculosis families, including Latin American-Mediterranean, Harlem, and Beijing. These findings suggest a wide genetic diversity of M. tuberculosis isolates at one outpatient clinic. A detailed molecular epidemiology survey is now warranted, especially following second massive immigration for local Panama Canal expansion activities. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1
new file mode 100644
index 00000000..e583bdef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.a1
@@ -0,0 +1,2 @@
+T1	Title 0 50	Wolbachia endosymbionts and human disease control.
+T2	Paragraph 51 1319	Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt
new file mode 100644
index 00000000..8530c352
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25046729.txt
@@ -0,0 +1,3 @@
+Wolbachia endosymbionts and human disease control.
+Most human filarial nematode parasites and arthropods are hosts for a bacterial endosymbiont, Wolbachia. In filaria, Wolbachia are required for normal development, fertility and survival, whereas in arthropods, they are largely parasitic and can influence development and reproduction, but are generally not required for host survival. Due to their obligate nature in filarial parasites, Wolbachia have been a target for drug discovery initiatives using several approaches including diversity and focused library screening and genomic sequence analysis. In vitro and in vivo anti-Wolbachia antibiotic treatments have been shown to have adulticidal activity, a long sought goal of filarial parasite drug discovery. In mosquitoes, it has been shown that the presence of Wolbachia can inhibit the transmission of certain viruses, such as Dengue, Chikungunya, Yellow Fever, West Nile, as well as the infectivity of the malaria-causing protozoan, Plasmodium and filarial nematodes. Furthermore, Wolbachia can cause a form of conditional sterility that can be used to suppress populations of mosquitoes and additional medically important insects. Thus Wolbachia, a pandemic endosymbiont offers great potential for elimination of a wide-variety of devastating human diseases. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1
new file mode 100644
index 00000000..3debc844
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.a1
@@ -0,0 +1,6 @@
+T1	Title 0 159	Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+T2	Paragraph 160 332	To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+T3	Paragraph 333 431	Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+T4	Paragraph 432 909	We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+T5	Paragraph 910 1379	Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+T6	Paragraph 1380 1641	We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt
new file mode 100644
index 00000000..4531b4d4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25179651.txt
@@ -0,0 +1,7 @@
+Emergence and prevention measures for multidrug resistant Pseudomonas aeruginosa in catheter-associated urinary tract infection in spinal cord injury patients.
+To evaluate measures for preventing multidrug resistant Pseudomonas aeruginosa (MDRP) in catheter-associated urinary tract infection (CAUTI) in spinal cord injury patients.
+Spinal Cord Injury Unit of Hyogo Prefectural Hyogo Prefectural Rehabilitation Center, Kobe, Japan.
+We defined MDRP as resistance to amikacin, imipenem and levofloxacin. We had eight cases of MDRP-causing CAUTI in hospitalized neurogenic bladder patients caused by spinal cord injury in 2 months. Pulse-field gel electrophoresis (PFGE) was performed for epidemiological studies. We assessed prevention measures against MDRP emergence from the 2nd month, such as surveillance of CAUTI and infection control, and evaluated the outcomes of these measures over a total of 8 months.
+Our PFGE results showed that these eight MDRP isolates could be considered as closely related strains. We concluded that this was an MDRP outbreak that was causing CAUTI. The isolated ratio of MDRP began to decrease over 4 months of surveillance and significantly decreased in the 4th quarter (7th and 8th months) compared with the 1st quarter (1st and 2nd months) (P=0.021) even though urinary tract device usage significantly increased over the same period (P<0.001).
+We experienced an outbreak of emergent MDRP causing CAUTI in neurogenic bladder patients with spinal cord injury. Our preventive measures for isolating the outbreak, including surveillance, may have led to the decrease we observed in the ratio of MDRP isolated.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1
new file mode 100644
index 00000000..041d11e5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.a1
@@ -0,0 +1,2 @@
+T1	Title 0 77	Biocontainment of genetically modified organisms by synthetic protein design.
+T2	Paragraph 78 1132	Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt
new file mode 100644
index 00000000..5e1fb9c1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25607366.txt
@@ -0,0 +1,3 @@
+Biocontainment of genetically modified organisms by synthetic protein design.
+Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1
new file mode 100644
index 00000000..4c1ed6f7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+T2	Paragraph 89 1701	Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt
new file mode 100644
index 00000000..7c86914f
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-25644009.txt
@@ -0,0 +1,3 @@
+Comparative genome sequencing of Rickettsia rickettsii strains that differ in virulence.
+Rickettsia rickettsii is an obligate intracellular pathogen that is the causative agent of Rocky Mountain spotted fever. Strains of R. rickettsii differ dramatically in virulence. In a guinea pig model of infection, the severity of disease as assessed by fever response varies from the most virulent, Sheila Smith, to Iowa, which causes no fever. To identify potential determinants of virulence in R. rickettsii, the genomes of two additional strains were sequenced for comparison to known sequences (comparative genome sequencing [CGS]). R. rickettsii Morgan and R strains were compared to the avirulent R. rickettsii Iowa and virulent R. rickettsii Sheila Smith strains. The Montana strains Sheila Smith and R were found to be highly similar while the eastern strains Iowa and Morgan were most similar to each other. A major surface antigen, rickettsial outer membrane protein A (rOmpA), is severely truncated in the Iowa strain. The region of ompA containing 13 tandem repeats was sequenced, revealing only seven shared SNPs (four nonsynonymous) for R and Morgan strains compared to Sheila Smith, with an additional 17 SNPs identified in Morgan. Another major surface antigen and autotransporter, rOmpB, exhibits a defect in processing in the Iowa strain such that the beta fragment is not cleaved. Sequence analysis of ompB reveals identical sequences between Iowa and Morgan strains and between the R and Sheila Smith strains. The number of SNPs and insertions/deletions between sequences of the two Montana strains and the two eastern strains is low, thus narrowing the field of possible virulence factors. 
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1
new file mode 100644
index 00000000..f56bb1b0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.a1
@@ -0,0 +1,2 @@
+T1	Title 0 143	Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+T2	Paragraph 144 1366	Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt
new file mode 100644
index 00000000..0f6102ce
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-26155675.txt
@@ -0,0 +1,3 @@
+Production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching.
+Here, we described the production of a cellulase-free alkaline xylanase from Bacillus pumilus MTCC 5015 by submerged fermentation and its application in biobleaching. Various process parameters affecting xylanase production by B. pumilus were optimized by adopting a Plackett-Burman design (PBD) as well as Response surface methodology (RSM). These statistical methods aid in improving the enzyme yield by analysing the individual crucial components of the medium. Maximum production was obtained with 4% yeast extract, 0.08% magnesium sulphate, 30 h of inoculum age, incubation temperature of 33.5 degrees C and pH 9.0. Under optimized conditions, the xylanase activity was 372 IU/ml. Media engineering improved a 5-fold increase in the enzyme production. Scanning electron microscopy (SEM) showed significant changes on the surface of xylanase treated pulps as a result of xylan hydrolysis. Increased roughness of paper carton fibres was apparent in scanning electron micrograph due to opening of the micro fibrils present on the surface by xylanase action. The untreated pulp did not show any such change. These results demonstrated that the B. pumilus MTCC 5015 xylanase was effective in bio-bleaching of paper carton.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1
new file mode 100644
index 00000000..8b317718
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.a1
@@ -0,0 +1,2 @@
+T1	Title 0 63	Carriage of Haemophilus influenzae in healthy Gambian children.
+T2	Paragraph 64 1585	1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt
new file mode 100644
index 00000000..08dfa697
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-2617654.txt
@@ -0,0 +1,3 @@
+Carriage of Haemophilus influenzae in healthy Gambian children.
+1240 throat samples were processed during different seasons in 11 different communities of The Gambia (West Africa). The carriage rate for Haemophilus influenzae type b ranged from 0 to 33%, but often attained 10% or more, higher than that reported from other open communities. The duration of carriage was short (less than 3 months) and H. influenzae b was found in only 10% of the carriers isolated during the previous or the following survey. Children less than 5 years old carried H. influenzae b in their throat significantly more often than children older than 14 years (P less than 0.05). A high carriage rate did not correlate with the wet or dry season. The carriage rate of children in rural areas was similar to that of children in urban areas. Children in day-care centres or nurseries had a surprisingly low carriage rate (2%). The carriage rate of H. influenzae b was compared to the presence of H. influenzae subspecies in a random sample, which revealed that H. influenzae subspecies was found in 90% of the children under 5 years old. Encapsulated strains of H. influenzae were found in 25% of the same sample, two-thirds of which were not type b. All capsule types were represented. No meningitis cases occurred in the survey populations. We conclude that the prevalence of H. influenzae b in open Gambian communities is similar to that in closed communities elsewhere, but that the kinetics are different from those in closed communities, as persistence of infection in Gambian children is short-lived.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1
new file mode 100644
index 00000000..b5402475
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+T2	Paragraph 103 1367	To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt
new file mode 100644
index 00000000..d635eef0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3015879.txt
@@ -0,0 +1,3 @@
+Construction of a host-vector system in Candida maltosa by using an ARS site isolated from its genome.
+To construct a host-vector system in an n-alkane-assimilating yeast, Candida maltosa, the isolation of an ARS site from its genome which replicates autonomously in C. maltosa was attempted. Leu- mutants of C. maltosa were transformed with a gene library prepared by using YEp13 (LEU2+) as a vector, and Leu+ transformants were obtained at a high frequency. A plasmid named pCS1 was isolated from the recipient cells. pCS1 contained a 6.3-kilobase (kb) fragment of the C. maltosa genome, and a 3.8-kb fragment with ARS activity was subcloned and designated the TRA (transformation ability) region. Vectors (pTRA1 and pTRA11) for C. maltosa J288 were constructed that contained this 3.8-kb fragment, pBR322, and the LEU2 gene of Saccharomyces cerevisiae. Transformation of C. maltosa J288 with these plasmids was successful by both spheroplast and lithium acetate methods. Southern blot analysis suggested that the copy number of pTRA1 in C. maltosa was between 10 and 20, and it was stably maintained during growth without selective pressure in the medium. It was also found that these vectors could transform S. cerevisiae leu2- to LEU2+, suggesting that the TRA region contained an ARS site(s) that was specific not only for C. maltosa but also for S. cerevisiae.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1
new file mode 100644
index 00000000..fd5a0422
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 94	Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+T2	Paragraph 95 950	An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt
new file mode 100644
index 00000000..c8fc4db2
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-3516874.txt
@@ -0,0 +1,3 @@
+Identification of a nonfimbrial adhesive factor of an enterotoxigenic Escherichia coli strain.
+An enterotoxigenic Escherichia coli strain (strain 2230), isolated from a patient with acute infantile diarrhea, was found to adhere only to the brush border of human intestinal epithelial cells. This strain does not hemagglutinate human, bovine, chicken, or guinea pig erythrocytes. The adhesion of E. coli 2230 appears to be mediated by a nonfimbrial bacterial surface protein of 16,000 daltons which can be extracted by heating the bacteria at 60 degrees C for 20 min. This surface protein is implicated as an adhesive factor because pretreatment of enterocytes with this protein extract completely inhibits the adhesion of E. coli 2230. This adhesive factor is serologically distinct from other adhesive factors found in enterotoxigenic E. coli strains. A plasmid DNA of 66 megadaltons is involved in the synthesis of this nonfimbrial adhesive factor.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1
new file mode 100644
index 00000000..7c5e11a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.a1
@@ -0,0 +1,2 @@
+T1	Title 0 88	Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+T2	Paragraph 89 1142	The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt
new file mode 100644
index 00000000..e1848509
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7867953.txt
@@ -0,0 +1,3 @@
+Cloning, sequence and regulation of expression of the lexA gene of Aeromonas hydrophila.
+The lexA gene of Aeromonas hydrophila (Ah) has been isolated by using a specific one-step cloning system. The Ah LexA repressor is able to block Escherichia coli (Ec) SOS gene expression and is likely to be cleaved by the activated RecA protein of this bacterial species after DNA damage. Ah lexA would encode a protein of 207 amino acids (aa), which is 75% identical to the LexA repressor of Ec. Two Ec-like SOS boxes have been located upstream from Ah lexA, the distance between them being 4 bp, whereas this same distance in Ec lexA is 5 bp. The structure and sequence of the DNA-binding domain of the LexA repressor of Ec, as well as the region at which its hydrolysis occurs, are highly conserved in Ah LexA. Moreover, a residue of the region implicated in the specific cleavage reaction, and which is present in all known RecA-cleavable repressors, is changed in the Ah LexA. Expression of Ah lexA is DNA-damage inducible in both the Ah and Ec genetic backgrounds to the same extent. In contrast, Ec lexA is poorly induced in DNA-injured Ah cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1
new file mode 100644
index 00000000..e8ef76d1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.a1
@@ -0,0 +1 @@
+T1	Title 0 44	The spread of Vibrio cholerae O139 in India.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt
new file mode 100644
index 00000000..b0aba7a1
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-7876637.txt
@@ -0,0 +1,2 @@
+The spread of Vibrio cholerae O139 in India.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1
new file mode 100644
index 00000000..e4e16ad5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.a1
@@ -0,0 +1,2 @@
+T1	Title 0 102	Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+T2	Paragraph 103 870	Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt
new file mode 100644
index 00000000..39574a93
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-817056.txt
@@ -0,0 +1,3 @@
+Tissue dispersion, cell harvest and fluid suspension culture by the use of bacterial neutral protease.
+Bacterial neutral protease of Bacillus polymyxa was found to disperse mammalian tissues and cells. Primary cell cultures were obtained from several tissues after treatments with 200 to 2,000 Kunitz unit per ml of this protease in either a phosphate buffer solution, a balanced salt solution or a tissue culture medium supplemented with serum. Monolayer cultures wither in their early passage levels or of established strains were harvested by a treatment with this protease, and proliferated again in monolayer after its removal. A growing culture of strain L-929 was kept in monodisperse suspension in the presence of this protease. In contrast to trypsin, this protease was found active in the presence of serum, stable during incubation and scarcely injured cells.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1
new file mode 100644
index 00000000..5e07107a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.a1
@@ -0,0 +1,2 @@
+T1	Title 0 101	Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+T2	Paragraph 102 1152	Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt
new file mode 100644
index 00000000..429d9ff3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8406892.txt
@@ -0,0 +1,3 @@
+Virulence determinants in nontoxinogenic Escherichia coli O157 strains that cause infantile diarrhea.
+Ten sorbitol-fermenting Escherichia coli O157 strains that cause infantile diarrhea and are positive in the fluorescence actin staining test were determined to be negative for Shiga-like toxin (SLT) genes. We amplified their complete eae genes, contrasting them with those of SLT-producing E. coli O157 by restriction fragment length polymorphism analysis and nucleotide sequence analysis of a 400-bp stretch of the 3' end of eae. The data substantiated the presence of two eae genotypes within serogroup O157, one resembling eae of enteropathogenic E. coli (EPEC) strain E2348/69, found in nontoxinogenic E. coli O157 strains, and the other resembling eae of EHEC strain EDL 933, found in toxinogenic E. coli O157 strains. Another EPEC-specific virulence determinant was also shown to be large plasmids harboring EPEC adherence factor sequences. The SLT-negative E. coli O157 strains described here fall under the heading of EPEC, which serves as an explanation for their virulence in infants, and represent a third pathogroup within serogroup O157.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1
new file mode 100644
index 00000000..7d1528ab
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.a1
@@ -0,0 +1,2 @@
+T1	Title 0 78	Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+T2	Paragraph 79 1701	The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt
new file mode 100644
index 00000000..801c1727
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-8698477.txt
@@ -0,0 +1,3 @@
+Macrophages exposed to Borrelia burgdorferi induce Lyme arthritis in hamsters.
+The mechanism(s) by which Lyme arthritis is induced has not been elucidated. In this study, we showed that macrophages have a direct, effector role in the pathogenesis of Lyme arthritis. Severe destructive arthritis was induced in recipients of macrophages obtained from Borrelia burgdorferi-vaccinated and nonvaccinated hamsters exposed to Formalin-inactivated B. burgdorferi in vitro and then challenged with the Lyme spirochete. Swelling of the hind paws was detected within 8 h of infection, increased rapidly, and peaked at 21 h. This initial swelling decreased, and by day 4 only slight swelling was detected. Severe swelling of the hind paws was detected 8 days after infection and increased rapidly, with peak swelling occurring on day 11. Histopathologic examination affirmed that macrophages exposed to Formalin-inactivated spirochetes induced a severe destructive Lyme arthritis. The onset and severity of the severe destructive arthritis were dependent on the number of macrophages transferred. By contrast, macrophages not exposed to Formalin-inactivated B. burgdorferi failed to induce severe destructive arthritis in recipients after challenge with B. burgdorferi. Similarly, severe destructive arthritis was not detected in recipients of macrophages injected with spirochetal growth medium. Our results also showed that transferred macrophages could not protect hamsters from infection with B. burgdorferi, as spirochetes were readily recovered from their tissues when cultured. These findings demonstrate that macrophages exposed to B. burgdorferi are directly involved in the induction of Lyme arthritis.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1
new file mode 100644
index 00000000..33822ed9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.a1
@@ -0,0 +1,2 @@
+T1	Title 0 59	Neuraminidase (sialidase) activity of Haemophilus parasuis.
+T2	Paragraph 60 993	Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt
new file mode 100644
index 00000000..73fca54b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9231420.txt
@@ -0,0 +1,3 @@
+Neuraminidase (sialidase) activity of Haemophilus parasuis.
+Neuraminidase (sialidase), a potential virulence factor in bacteria, was demonstrated in Haemophilus parasuis, an invasive swine pathogen, but not in four other pathogens of the Pasteurellaceae family: H. influenzae, H. somnus, H. paragallinarum, or Actinobacillus pleuropneumoniae. H. parasuis neuraminidase had an acidic pH optimum and a specificity for several substrates also cleaved by other bacterial neuraminidases. Similar to the neuraminidase of Pasteurella multocida, H. parasuis neuraminidase was cell associated and did not require divalent cations for activity. Exogenous sialic acid added to growth medium of H. parasuis was cleared after a lag of about 10 h and these cultures grew to a greater final density than cultures without added sialic acid, indicating that exogenous sialic acid is metabolized. The role of sialidase in providing nutrients to H. parasuis may be an important factor in its obligate parasitism.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1
new file mode 100644
index 00000000..c0447347
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.a1
@@ -0,0 +1,2 @@
+T1	Title 0 133	Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+T2	Paragraph 134 1567	Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt
new file mode 100644
index 00000000..a6e54ac0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9562874.txt
@@ -0,0 +1,3 @@
+Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.
+Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1
new file mode 100644
index 00000000..9a792678
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.a1
@@ -0,0 +1,2 @@
+T1	Title 0 180	[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+T2	Paragraph 181 4181	The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt
new file mode 100644
index 00000000..d1cd81c3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9575437.txt
@@ -0,0 +1,3 @@
+[Comparative studies on activities of antimicrobial agents against causative organisms isolated from patients with urinary tract infections (1996). I. Susceptibility distribution].
+The frequencies of isolation and susceptibilities to antimicrobial agents were investigated on 680 bacterial strains isolated from patients with urinary tract infections (UTIs) in 10 hospitals during the period of June 1996 to May 1997. Of the above bacterial isolates, Gram-positive bacteria accounted for 30.4% and a majority of them were Enterococcus faecalis. Gram-negative bacteria accounted for 69.6% and most of them were Escherichia coli. Susceptabilities of several isolated bacteria to antimicrobial agents were as followed; 1. Enterococcus faecalis Ampicillin (ABPC) showed the highest activity against E. faecalis isolated from patients with UTIs. Its MIC90 was 1 microgram/ml. Imipenem (IPM) and vancomycin (VCM) were also active with the MIC90S of 2 micrograms/ml. The others had low activities with the MIC90S of 16 micrograms/ml or above. 2. Staphylococcus aureus including MRSA Arbekacin (ABK) and VCM showed the highest activities against both S. aureus and MRSA isolated from patients with UTIs. The MIC90S of them were 1 or 2 micrograms/ml. The others except minocycline (MINO) had low activities with the MIC90S of 32 micrograms/ml or above. 3. Staphylococcus epidermidis ABK and VCM showed the strongest activities against S. epidermis isolated from patients with UTIs. The MICs for all strains were equal to or lower than 2 micrograms/ml. Cefazolin (CEZ), cefotiam (CTM) and cefozopran (CZOP) were also active with the MIC90S of 4 micrograms/ml. Compared with antimicrobial activities of cephems is 1995, the MIC90S of them had changed into a better state. They ranged from 4 micrograms/ml 16 micrograms/ml in 1996. 4. Streptococcus agalactiae All drugs except MINO were active against S. agalactiae. ABPC, CZOP, IPM, and clarithromycin (CAM) showed the highest activities. The MICs for all strains were equal to or lower than 0.125 micromilligrams. Tosufloxacin (TFLX) and VCM were also active with the MIC90S of 0.5 micromilligrams. 5. Citrobacter freundii Gentamicin (GM) showed the highest activity against C. freundii isolated from patients with UTIs. Its MIC90 was 0.5 micrograms/ml. IPM and amikacin (AMK) were also active with the MIC90S of 1 microgram/ml and 2 micrograms/ml, respectively. Cefpirome (CPR) and CZOP were also active with the MIC90S of 8 micrograms/ml. The MIC90S of the others were 16 micrograms/ml or above. 6. Enterobacter cloacae IPM showed the highest activity against E. cloacae. The MICs for all strains were equal to or lower than 0.5 microgram/ml. The MIC90S of ciprofloxacin (CPFX) and TFLX were 1 microgram/ml, the MIC90 of AMK was 2 micrograms/ml, the MIC90S of CZOP, GM and ofloxacin (OFLX) were 4 micrograms/ml. The MIC50S of cephems except CEZ, cefmetazole (CMZ) and cefaclor (CCL) had changed into a better state in 1996, compared with those in 1995. 7. Escherichia coli All drugs except penicillins and MINO were active against E. coli. Particularly CPR, CZOP and IPM showed the highest activities against E. coli. The MIC90S of them were 0.125 microgram/ml or below. Among E. coli strains, those with low susceptibilities to cephems except CEZ, cefoperazone (CPZ), latamoxef (LMOX) and CCL have increased in 1996, compared with those in 1995. 8. Klebsiella pneumoniae K. pneumoniae was susceptible to all drugs except penicillins, with the MIC90S of 2 micrograms/ml or below. CPR had the strongest activity, the MICs for all strains were equal to or lower than 0.25 microgram/ml. Flomoxef (FMOX), cefixime (CFIX), CZOP and carumonam (CRMN) were also active with the MIC90S of 0.125 microgram/ml or below. 9. Pseudomonas aeruginosa All drugs except quinolones were not so active against P. aeruginosa with the MIC90S were 32 micrograms/ml or above. Quinolones were more active in 1996 than 1995. The MIC90S of them were between 4 micrograms/ml and 8 micrograms/ml, and the MIC50S of them were between 1 microgram/ml and 2 micrograms/ml. 10. Serratia marcescens GM showed the highest activity against S. marcescens. Its MIC90 was 1 micro
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1
new file mode 100644
index 00000000..5d0d21d7
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.a1
@@ -0,0 +1,6 @@
+T1	Title 0 98	Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+T2	Paragraph 99 132	Experimental murine tuberculosis.
+T3	Paragraph 133 297	To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+T4	Paragraph 298 583	Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+T5	Paragraph 584 1218	Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+T6	Paragraph 1219 1399	Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt
new file mode 100644
index 00000000..098ffd30
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-9666962.txt
@@ -0,0 +1,7 @@
+Effect of cytokine modulation by thalidomide on the granulomatous response in murine tuberculosis.
+Experimental murine tuberculosis.
+To evaluate the effect of cytokine modulation by thalidomide on the progression of the lung granulomatous response following aerosol tuberculosis infection in mice.
+Mice infected by the respiratory route with 200-500 viable Mycobacterium tuberculosis Erdman were treated with daily subcutaneous injections of thalidomide (30 mg/kg) or saline for 4 weeks. The bacillary load, granulomatous response and cytokine production in the lungs were evaluated.
+Aerosol M. tuberculosis infection resulted in a progressive granulomatous response in the lungs. At 28 days after infection, large granulomata with central necrosis and no apoptosis were observed. The infection induced high serum and lung cytokine mRNA levels. Thalidomide treatment resulted in a significant reduction in tumor necrosis factor-alpha, interleukin 6 (IL-6) and IL-10 protein levels (blood) and mRNA expression (lungs). IL-12 and interferon-gamma were unaffected. The lungs of thalidomide-treated mice had smaller granulomata with apoptotic cells and no necrosis. Thalidomide treatment did not change the bacillary load.
+Thalidomide immunomodulation reduces inflammatory cytokines and concomitant lung pathology following acute aerosol M. tuberculosis infection, without increasing the bacillary load.
+
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt
new file mode 100644
index 00000000..2adcc35b
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-000.txt
@@ -0,0 +1,3 @@
+Eighty-eight strains belonging to 10 species of lactic acid bacteria 
+(LAB) isolated from traditional Italian cheeses were studied for their 
+reduction activity: Enterococcus faecalis, Enterococcus faecium, Enterococcus durans, Streptococcus thermophilus, Lactococcus lactis ssp. lactis, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. bulgaricus, Lactobacillus helveticus and Pediococcus pentosaceus. It was observed that the lactococci reached minimum redox potential before the lactobacilli. The reduction rate of Enterococcus spp. and L. lactis ssp. lactis was higher than that of the streptococci and Lactobacillus spp. All the P. pentosaceus strains had poor reduction activity compared with the other species.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt
new file mode 100644
index 00000000..003ac922
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-001.txt
@@ -0,0 +1,32 @@
+The E. faecalis strains were characterized by a relevant reduction power. In fact, this species showed the lowest Ehmin (−221 ± 13·4 mV), the largest Δmax (326 ± 93·1 mV), and was the fastest to reach Δmax (t*: 1·1 ± 0·3 h) (Table 2). The behaviour of the 10 strains was the same except for VS368, which was the most rapid E. faecalis strain (t*: 0·5 h) and, at the same time, the one showing the highest Ehmin (−189 mV). At 37°C, the mean curves for E. faecium, E. durans and L. lactis ssp. lactis
+ had similar Eh evolution (sharp decrease around the second hour of 
+culture), but the minimum values were different. The strains of L. lactis ssp. lactis were more reducing than the strains of the other two species: Ehmin: −162 ± 32·9 mV vs−138 ± 31·3 and −120 ± 29·0, respectively (Fig. 2). The 10 strains of E. faecium
+ had similar reduction power, although after 24 h of incubation 
+three strains, FK5, FK6 and FK7, isolated from Scimudin cheese, showed 
+higher reducing activity than the other seven. The slowest and least 
+reducing strain, 174, was isolated from Caciocavallo Ragusano cheese. 
+The E. durans strains showed similar Eh evolution over 
+24 h, except for VS263 isolated from Formagèla Valseriana cheese. 
+VS263 was the fastest to achieve Ehmin and Δmax (tmin: 2·0 h; t*: 1·0 h) and had higher reduction power (Ehmin: −171 mV) than the others. The L. lactis ssp. lactis strains had the highest reduction activity after the E. faecalis strains. Their Ehmin values were: −162 ± 32·9 mV, and they were characterized by a rapid decrease in tmin 3·8 ± 0·8 h and t*
+ 2·2 ± 0·3 h. Once again ‘atypical’ behaviour was 
+detected in the strains isolated from Formagèla Valseriana, namely VS179
+ and VS180, these being revealed to have lower reduction power compared 
+with the other lactococci belonging to the same species. Streptococcus thermophilus,
+ the major species used as the starter culture in cheese manufacture, 
+was the slowest of the tested LAB species. Its reduction activity 
+increased constantly, and it consequently had a smaller Δmax; all the strains reached Ehmin
+ at the end of the 24-h incubation period, the exception being O2A 
+isolated from Fontina, found to be the most reducing and reaching Ehmin after 14 h. Instead, strain LOD11 was the slowest S. thermophilus strain (t*: 4·5 h), however it also had the highest Ehmin (−45 mV). Among the lactobacilli, the highest reducing species was L. paracasei ssp. paracasei: their strains showed the lowest Ehmin (−169 ± 13·8 mV), and were the fastest to achieve Δmax (4·2 ± 1·3 h). The B1B strain showed similar behaviour to the enterococci (Ehmin: −186; t*: 3 h) (Table 3). On the contrary, the BB3 strain isolated from Formai de Mut cheese was very slow: it took 12 h to reach Ehmin. The redox curve of L. paracasei ssp. paracasei, comparable with that of E. faecalis and reaching similar final values, shows a more gradual slope (lower Δmax) reached over longer times. With regard to the strains of L. plantarum,
+ the redox potential course is characterized by an initial stabilizing 
+period followed by a rapid and consistent decrease corresponding to the 
+major Δmax (229 ± 88·6 mV) found among the 
+tested lactobacilli. This species showed good reduction power and was as
+ fast in reaching Δmax as L. paracasei ssp. paracasei. The lowest reducing lactobacilli were found to be L. delbrueckii ssp. bulgaricus and L. helveticus (Ehmin: −54 ± 20·4 mV and −54 ± 23·8 mV). Furthermore, for both the thermophilic lactobacilli species, Eh decreased slowly (L. delbrueckii ssp. bulgaricus: t*: 6·0 ± 1·7 h and L. helveticus t*: 6·4 ± 1·6 h), the mean curves showing similar evolution over the 24-h period. All the strains of P. pentosaceus had poor reduction activity. In fact, they showed the highest Ehmin (−59 ± 23·5 mV), the smallest Δmax (24 ± 8·9 mV) and were the slowest to achieve Δmax
+ (5 ± 2·2 h). Most of the selected isolates for this 
+investigation came from cheeses produced in the mountains, and it is 
+interesting to note that the majority of the strains from Scimudin 
+cheese (77·7%) were the fastest to achieve Ehmin, while the 
+strains isolated from Formai de Mut took more time to reach the minimum 
+Eh value. Isolated from Formagèla Valseriana were the strains L. lactis ssp. lactis and E. durans;
+ these strains, except for VS263, showed lower reduction power than the 
+other strains of the same species, but, nevertheless, took less time.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt
new file mode 100644
index 00000000..ac3467cb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-002.txt
@@ -0,0 +1,4 @@
+The second component has a heavy loading only for t* (0·61). Indeed, we immediately identified distinct groups of strains corresponding to Enterococcus spp., L. lactis ssp. lactis; L. paracasei ssp. paracasei, L. plantarum, thermophilic lactobacilli (L. delbrueckii ssp. bulgaricus, L. helveticus) and S. thermophilus and, furthermore, noted important differences among the strains of the same species. As can be seen from Fig. 4, E. faecalis, E. faecium, E. durans and L. lactis ssp. lactis were placed in quadrant 3, while L. paracasei ssp. paracasei and L. plantarum
+ were in quadrant 2. In fact, both groups are associated with high 
+reduction activity, and the species tend to fall on the left side of the
+ plot where the variable corresponding to Δmax was located.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt
new file mode 100644
index 00000000..1cb08b82
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-003.txt
@@ -0,0 +1,4 @@
+Considerable
+ variation was found among the 10 different species tested for their 
+ability to change the redox potential. The species studied in this paper
+ are those most frequently present in raw milk cheeses (Enterococcus spp., Pediococcus spp. and L. lactis ssp. lactis), those used to make starter cultures (S. thermophilus, L. delbrueckii ssp. bulgaricus and L. helveticus), and species considered as probiotic bactera (L. paracasei subsp. paracasei and L. plantarum).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt
new file mode 100644
index 00000000..66bf0cb0
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-17953562-004.txt
@@ -0,0 +1,2 @@
+Among the cocci the most reducing species was, by far, E. faecalis, and among the rods L. paracasei ssp. paracasei. The nonpathogen enterococci and L. lactis ssp. lactis reach Eh values of −120 and −220 mV in a very short time (about 3–4 h), while S. thermophilus and L. delbrueckii ssp. bulgaricus, species found in starter cultures, are characterized by a lower reducing power. Also the species considered as probiotics (L. paracasei ssp. paracase and L. plantarum)
+ showed good reducing power.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt
new file mode 100644
index 00000000..a99f21a3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-000.txt
@@ -0,0 +1 @@
+•Carnobacterium maltaromaticum has been isolated from atypical soft cheese.•Its presence in cheese caused the decrease in the concentration of Psychrobacter sp.•Cellular concentration of C. maltaromaticum was the main factor involved in the inhibition.•This produced malty/chocolate like aroma due to 3-methylbutanal in milk.•This species could play a major role as cheese ripening flora.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt
new file mode 100644
index 00000000..5c30301e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-001.txt
@@ -0,0 +1,10 @@
+Carnobacterium maltaromaticum
+ is a lactic acid bacterium isolated from soft cheese. The objective of 
+this work was to study its potential positive impact when used in cheese
+ technology. Phenotypic and genotypic characterization of six strains of
+ C. maltaromaticum showed that they belong to different 
+phylogenetic groups. Although these strains lacked the ability to 
+coagulate milk quickly, they were acidotolerant. They did not affect the
+ coagulation capacity of starter lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus, used in dairy industry. The impact of C. maltaromaticum LMA 28 on bacterial flora of cheese revealed a significant decrease of Psychrobacter
+ sp. concentration, which might be responsible for cheese aging 
+phenomena.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt
new file mode 100644
index 00000000..a31894ef
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-002.txt
@@ -0,0 +1 @@
+Cellular concentration of C. maltaromaticum LMA 28 was found to be the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt
new file mode 100644
index 00000000..a983208c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-003.txt
@@ -0,0 +1,5 @@
+The presence of an opportunistic psychrotrophic LAB named Carnobacterium maltaromaticum
+ has been demonstrated in numerous French cheeses (Appellation d'Origine
+ Protégée, AOP = Protected Designation of Origin, PDO) at the 
+end of ripening and cold storage, without affecting the final product 
+quality ( Cailliez-Grimal et al., 2007 and Millière et al., 1994).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt
new file mode 100644
index 00000000..ee487621
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-004.txt
@@ -0,0 +1 @@
+Many Carnobacterium strains have been used previously as protective cultures against pathogenic bacteria (for instance Listeria monocytogenes) in fish and meat products ( Brillet et al., 2005, Duffes et al., 1999, Matamoros et al., 2009 and Vescovo et al., 2006). The bacteriocin-producing ability of Carnobacterium strains was found to play a key role in controlling spoilage and pathogenic bacteria in food and in in vitro model systems ( Dos Reis et al., 2011, Martin-Visscher et al., 2011 and Bernardi et al., 2011), while external factors, including pH, salt and storage temperatures, were also shown to have a significant impact ( Hwang, 2009 and Leroi et al., 2012).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt
new file mode 100644
index 00000000..e7a16aaf
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-005.txt
@@ -0,0 +1,4 @@
+The differentiation of the 6 strains of C. maltaromaticum,
+ isolated from soft cheeses was performed using biochemical and 
+genotypic tests. A comparison of their biochemical characteristics 
+showed weak differences in their fermentation pattern (data not shown).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt
new file mode 100644
index 00000000..6a2596ee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-006.txt
@@ -0,0 +1,4 @@
+In
+ the conditions tested, all the strains were able to produce 
+3-methylbutanal in milk cultured at 4 °C and at 30 °C after 
+24 h of incubation (Table 4). Milk bottles tasted and smelled significantly differently (P < 0.05) for each Carnobacterium species after 48 h. The taste panel could clearly distinguish the milk malty flavor in bottles inoculated with C. maltaromaticum LMA 28 and lactic and aromatic flavor with LMA 14. The other strains did not exhibit particular flavors. The strain C. maltaromaticum LMA 28 was tested for cheese assay.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt
new file mode 100644
index 00000000..e1d2ed50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-007.txt
@@ -0,0 +1 @@
+After 20 and 34 days of ripening, cheeses tasted and smelled significantly differently (P < 0.05) to the reference without C. maltaromaticum LMA 28. The taste panel clearly distinguished the malty and butyric flavor in cheeses inoculated with C. maltaromaticum LMA 28.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt
new file mode 100644
index 00000000..a3ff807a
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-008.txt
@@ -0,0 +1,2 @@
+Therefore, the increase in 
+the cellular concentration of C. maltaromaticum LMA 28 improved the inhibition of both Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110 in milk.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt
new file mode 100644
index 00000000..73c92c14
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-009.txt
@@ -0,0 +1,4 @@
+Although all strains of C. maltaromaticum have at least one gene encoding a bacteriocin, none of the target bacteria tested was inhibited by C. maltaromaticum
+ LMA 7 and LMA 14, suggesting that the gene was not expressed in the 
+culture conditions tested. The PFGE analysis showed that all the strains
+ were different from each other according to the criteria of  Tenover et al. (1995), showing a diversity of this species in the same biotope.In cheese industry, two species played a major role in the milk transformation into cheese i.e. L. lactis and S. thermophilus, which acidify and coagulate milk quickly.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt
new file mode 100644
index 00000000..f8d6f02d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-010.txt
@@ -0,0 +1,10 @@
+Different species of Psychrobacter
+ have been isolated from various ecosystems; cold or hot, slightly or 
+heavily salted, frozen sea, fish, refrigerated meat and from clinical 
+samples ( Bowman, 2006). In case of cheese, this bacterium could arise either from raw milk or environmental contamination. It belongs to the order Pseudomonadales,
+ well known in food microbiology as spoilage flora of dairy products 
+that exhibit high proteolytic activities. It could play a role in 
+accelerating the aging process of cheese. To reduce this process, C. maltaromaticum could be use as ripening flora.The study on the inhibition of the two target strains Psychrobacter sp. LMA 1 and L. monocytogenes CIP 82110, in milk predicted that the cellular concentration of C. maltaromaticum the most inhibiting factor resulted in high inhibitory growth response of Psychrobacter sp. and L. monocytogenes
+ in milk. However, the combination of other variables had also an 
+impact. The exact mechanism of inhibition is still unknown and deserves 
+further investigations.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt
new file mode 100644
index 00000000..879c78ec
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-24010601-011.txt
@@ -0,0 +1,15 @@
+The use of the strain C. maltaromaticum
+ LMA28 in cheese technology and its impact on the microflora of this 
+soft cheese has been demonstrated in this study. It presence caused a 
+decrease in the concentration of Psychrobacter sp., which might
+ be responsible for accelerating the aging phenomena of soft cheese. 
+Moreover, the cellular concentration of C. maltaromaticum LMA 28 was the main factor involved in the inhibition of Psychrobacter sp. and L. monocytogenes
+ CIP 82110 in our experimental conditions. However, the exact mechanism 
+of inhibition is still unknown and deserves further investigations. In 
+addition, C. maltaromaticum LMA 28 produced malty/chocolate-like aroma due to 3-methylbutanal from the catabolism of leucine ( Afzal et al., 2012).
+ However, it is essential to study its impact on proteolysis and 
+lipolysis during cheese ripening. Being psychrotrophic and 
+alkalinophilic, having antibacterial activity and an ability to increase
+ flavor, this species could play a major role as cheese ripening flora 
+with no negative interference on the starters currently used (for 
+instance S. thermophilus and L. lactis).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt
new file mode 100644
index 00000000..e7dd8995
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-000.txt
@@ -0,0 +1,13 @@
+However, 96.3 and 97.9%
+ of the total microbiota of the raw milk and pasteurized cheese rind, 
+respectively, were composed of species present in both types of cheese, 
+such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens
+ were present at low levels (0.5 and 1.6%, respectively) on the rind of 
+both the raw and the pasteurized milk cheeses, even though this 
+bacterium had been inoculated during the manufacturing process. 
+Interestingly, Psychroflexus casei, also described as giving a 
+red smear to Raclette-type cheese, was identified in small proportions 
+in the composition of the rind of both the raw and pasteurized milk 
+cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the 
+common species of bacteria reached more than 99%. The main species 
+identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt
new file mode 100644
index 00000000..2c474b4c
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-001.txt
@@ -0,0 +1,2 @@
+Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer
+ was present in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt
new file mode 100644
index 00000000..d2fd8ff4
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-002.txt
@@ -0,0 +1,5 @@
+Herve cheese is a soft cheese with a washed 
+rind, and is made from raw or pasteurized milk. Its texture is firm, 
+smooth, and creamy and it has a 45% minimum fat content. Its 
+characteristic flavor and orange-colored rind is attributed to the 
+presence of at least 1 bacterium: Brevibacterium linens
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt
new file mode 100644
index 00000000..bcfa0b50
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-003.txt
@@ -0,0 +1,7 @@
+Originally, Herve cheese was made from raw milk. Later, for safety reasons due to the potential presence of Listeria monocytogenes, Herve cheese made from pasteurized milk was developed.The
+ dominant microbiota present on red-smear cheeses such as Maroilles, 
+Muenster, Limburger, and Pont l’Évêque has previously been described as 
+being composed of gram-positive bacteria such as Micrococcus, Staphylococcus, and various coryneform species such as Corynebacterium spp., Arthrobacter spp., Rhodococcus spp., and B. linens ( Brennan et al., 2002; Feurer et al., 2004b).
+ However, the microbiota specific to Herve cheese has never previously 
+been fully explored. The orange rind of the cheese is attributed to 1 
+particular bacterium: B. linens.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt
new file mode 100644
index 00000000..eefc5855
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-004.txt
@@ -0,0 +1 @@
+The heart of the raw milk cheeses was composed of L. lactis ssp. cremoris (79.5%), Staphylococcus equorum (6.0%), Psychrobacter celer (5.7%), and Streptococcus salivarius ssp. thermophilus (4.1%). The heart of the pasteurized milk cheeses was mainly composed of L. lactis ssp. cremoris (76.87%), Psychrobacter sp. (11.35%), and Staph. equorum (6.57%).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt
new file mode 100644
index 00000000..f2fbaac3
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-005.txt
@@ -0,0 +1 @@
+The rind of the raw milk cheeses was mainly composed of Corynebacterium casei (51.17%), L. lactis ssp. cremoris (11.62%), Staph. equorum (5.54%), Marinilactibacillus psychrotolerans (4.55%), Vagococcus salmoninarum (3.16%), Psychrobacter spp. (2.94%), Fusobacterium spp. (2.54%), Clostridiisalibacter (2.48%), and Strep. salivarius (1.93%). Many other species were present at levels below 2% and these are presented in  Figure 3.The rind of the pasteurized milk cheeses was mainly composed of species also encountered in the raw milk cheeses, such as Psychrobacter (37.76%), L. lactis ssp. cremoris (10.76%), C. casei (7.42%), V. salmoninarum (5.69%), Staph. equorum (5.28%), Vibrio spp. (5.03%), Fusobacterium spp. (4.39%), M. psychrotolerans (3.69%), Pseudoalteromonas spp. (2.71%), Vagococcus fluvialis (2.64%), and Strep. salivarius (2.07%). Other species were present, including B. linens, but at percentages below 2% ( Figure 3).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt
new file mode 100644
index 00000000..1afb1005
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-006.txt
@@ -0,0 +1,2 @@
+Phylotypes specifically identified in the raw milk 
+cheese rind were mainly identified as Corynebacterium. Other phylotypes were identified as belonging to Streptococcus, Staphylococcus, or Vagococcus genera ( Supplementary Figure S1; http://dx.doi.org/10.3168/jds.2014-8225). On the other hand, phylotypes specifically identified in the pasteurized milk cheese rind were Psychrobacter spp., Pseudoalteromonas spp., and Vibrio spp. ( Supplementary Figure S2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt
new file mode 100644
index 00000000..0b55dcff
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-007.txt
@@ -0,0 +1 @@
+Corynebacterium casei was more present in the raw milk cheeses and this species was partially replaced by P. celer in the pasteurized milk cheeses.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt
new file mode 100644
index 00000000..84f6e6aa
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-008.txt
@@ -0,0 +1 @@
+Lactococcus lactis ssp. cremoris, widely described in cheeses ( Taïbi et al., 2011), was the main species identified in the hearts of both the raw milk and the pasteurized milk cheeses. Lactococcus lactis ssp. cremoris and C. casei were the main species identified in the raw milk cheese rinds, whereas Psychrobacter spp., L. lactis ssp. cremoris, and C. casei were the main species identified in the pasteurized milk cheese rinds.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt
new file mode 100644
index 00000000..ec52e098
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-009.txt
@@ -0,0 +1 @@
+Psychrobacter celer and Vibrio spp. populations were statistically more widely encountered in the pasteurized milk cheeses (P < 0.001 and P < 0.05, respectively; Figure 5a), whereas C. casei and Enterococcus faecalis were found more in the raw milk cheeses (P < 0.05; Figure 5a).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt
new file mode 100644
index 00000000..143b06ad
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-010.txt
@@ -0,0 +1,7 @@
+The presence of P. celer
+ has already been described previously and this bacterium contributes 
+significantly to the aromatic properties of cheese, as it influences 
+total volatile aroma production ( Irlinger et al., 2012). The presence of P. celer
+ in the cheeses studied here may be explained by its presence in the 
+saline water used in the manufacturing process. Indeed, this bacterium 
+was originally isolated from seawater ( Yoon et al., 2005). Vibrio spp. have not been reported frequently in cheese ( Feurer et al., 2004a) but some studies have suggested that these bacteria could play a role in the ripening process (El-Baradei et al., 2007). Moreover, a new Vibrio species, Vibrio casei, has even been isolated from the rind of red-smear cheeses ( Bleicher et al., 2010). The presence of C. casei found in the raw milk cheeses here is not surprising, as this has already been described previously ( Mounier et al., 2005).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt
new file mode 100644
index 00000000..b37006c8
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-011.txt
@@ -0,0 +1,3 @@
+However, the use of P. celer
+ as an indicator of pasteurized milk cheese should be undertaken with 
+care.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt
new file mode 100644
index 00000000..9cd59f24
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-012.txt
@@ -0,0 +1,8 @@
+Figure 6 shows that the fecal contaminant E. faecalis
+ was found to be present in the raw milk cheeses (0.6%) in the present 
+study but that its counts were very low in the pasteurized milk cheeses 
+(less than 0.05%). These differences are mainly due to the nature of the
+ milk used in raw milk cheeses, which may still be contaminated with 
+bacteria that are either a source of typicality (C. casei and E. faecalis) or a microbiological hazard (E. faecalis). Usually, the most common enterococci encountered in cheese are E. faecalis and Enterococcus faecium, with E. faecium being the most frequently occurring species in dairy cows ( Gelsomino et al., 2002). Indeed, E. faecium was identified in our raw milk cheese samples (0.3%). In addition, Enterococcus casseliflavus, already previously described in cheese ( Gelsomino et al., 2001, 2002),
+ was also detected in our samples (0.3% in raw milk cheeses and 0.1% in 
+pasteurized milk cheeses).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt
new file mode 100644
index 00000000..379766bb
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-013.txt
@@ -0,0 +1,7 @@
+Other phylotypes were also identified in some of the samples in the present study, such as Vagococcus spp. Vagococcus salmoninarum, a species first identified from salmonid fishes and closely related to the Carnobacterium genus ( Wallbanks et al., 1990), was identified in several of the raw milk cheese samples. Vagococcus fluvialis, previously isolated from animal and human sources ( Collins et al., 1989; Pot et al., 1994; Teixeira et al., 1997) and even from cheese (Callon et al., 2014), was also identified here.It was surprising to identify the pathogenic bacteria Morganella morganii, already previously described in milk or cheese ( Tornadijo et al., 1993; Delbès-Paus et al., 2012).
+ This bacterium, known to be able to produce biogenic amines such as 
+histamine, has been shown to be responsible for the production of 
+cadaverine in uncooked pressed cheeses (Delbès-Paus et al., 2012).Interestingly, the genus Citricoccus
+ was also identified. This bacterium has never previously been 
+identified in cheese, but it has been isolated several times from walls,
+ especially mold-colonized walls ( Altenburger et al., 2002; Schäfer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt
new file mode 100644
index 00000000..50b1dc7d
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-014.txt
@@ -0,0 +1 @@
+In addition, the presence of halophilic and alkaliphilic lactic acid bacteria was observed in the present study, such as M. psychrotolerans. This bacterium, initially isolated from marine organisms in certain areas of Japan ( Ishikawa et al., 2003), has already been previously described in cheese (Ishikawa et al., 2007) and is known to possess an anti-Listeria effect ( Roth et al., 2011). Another bacterium identified in our study of the genus Halomonas has also been reported in smear-ripened cheeses ( Mounier et al., 2005).The identification in our samples of Pseudoalteromonas was quite unexpected, as the presence of these bacteria in cheese has previously been reported only once ( Ogier et al., 2004).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt
new file mode 100644
index 00000000..a5023ee9
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-015.txt
@@ -0,0 +1 @@
+Brachybacterium faecium was also identified in our study. This bacterium is close to 2 other Brachybacterium species also identified once in both French Gruyere and Beaufort cheeses ( Schubert et al., 1996).Leucobacter spp., Alkalibacterium spp., Carnobacterium spp., and Raoultella planticola, already described in milk or cheese ( Herbin et al., 1997; Ishikawa et al., 2007; Larpin-Laborde et al., 2011; Roth et al., 2011; Zadoks et al., 2011), were also identified in the raw milk cheeses in the current study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt
new file mode 100644
index 00000000..46578535
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-016.txt
@@ -0,0 +1,10 @@
+A previous study reported that Psychroflexus casei gave a “red smear” color to Raclette-type cheese ( Seiler et al., 2012). Our hypothesis is that, in conjunction with B. linens
+ and other bacteria, this bacterium could play a role in the orange-red 
+coloration of Herve cheese. Indeed, in the raw and pasteurized cheeses 
+studied here, B. linens were not the dominant bacteria in the 
+rind (0.5 and 1.6% of raw and pasteurized rind microbiota, 
+respectively), even though these bacteria had been inoculated during the
+ manufacturing process. This result is in agreement with previous 
+studies reporting that B. linens was not a significant member 
+of the surface microbiota of smear cheese, even though it is still used 
+as the major component of ripening cultures ( Brennan et al., 2002; Gori et al., 2013). It is also possible that other preponderant bacteria such as Psychrobacter and Staphylococcus play a role in the coloration of smear cheeses. As described previously ( Hoppe-Seyler et al., 2007), the yellow-orange color of the rind of these cheeses could be due to interactions between pigmented or nonpigmented B. linens and yellow-pigmented Arthrobacter ( Ogier et al., 2004; Leclercq-Perlat and Spinnler, 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt
new file mode 100644
index 00000000..ee7affee
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25064656-017.txt
@@ -0,0 +1 @@
+One study reported the presence of Bavariicoccus seileri gen. nov., sp. nov. on the surface and in the smear water of German red-smear soft cheese ( Schmidt et al., 2009). However, this bacterium was not identified in our samples. Finally, a previous study also suggested that the color of B. linens depended on the yeast used for the deacidification of Muenster cheese ( Leclercq-Perlat et al., 2004). The presence of yeast was not, however, assessed in this study.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt
new file mode 100644
index 00000000..ab03e0f5
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-000.txt
@@ -0,0 +1 @@
+Enhancing vitamin B12 content in soy-yogurt by Lactobacillus reuteri
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt
new file mode 100644
index 00000000..7ea5ef75
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-001.txt
@@ -0,0 +1 @@
+Glycerol and fructose were confirmed to enhance the production of vitamin B12.•Glycerol and fructose induced the expression of cobT and cbiA.•Glycerol and fructose functioned to balance the redox reaction.•High content of fructose supplementation suppressed expression of cobT.•Vitamin B12 content in this soymilk is higher than other fermented soybean food.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt
new file mode 100644
index 00000000..d55a2a5e
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-002.txt
@@ -0,0 +1,10 @@
+More
+ attention from the aged and vegetarians has been paid to soy-product 
+due to its taste, easy digestibility, as well as the association with 
+health. However, soy-product has a defect of low vitamin content, mainly
+ the water-soluble vitamin B12. This study was to investigate co-fermentation of glycerol and fructose in soy-yogurt to enhance vitamin B12 production by Lactobacillus reuteri. After a serial combination experiments, the co-fermentation was confirmed to enhance the production of vitamin B12 up to 18 μg/100 mL. Both supplementations induced the expression of cobT and cbiA
+ and functioned to balance the redox reaction. Meanwhile, high content 
+of fructose supplementation reduced the production of vitamin B12 and suppressed expression of cobT in bacteria. It was proved that the vitamin B12
+ content of this soy-yogurt is higher than other fermented soybean based
+ food and thus can be served as an alternative food for the aged and 
+vegetarians.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt
new file mode 100644
index 00000000..f7fafc29
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-25955289-003.txt
@@ -0,0 +1,16 @@
+Watanabe et al. (2014)
+ reported that Japanese natto and Korean soybean products contain 0.1 to
+ 0.9 μg per 100 g. All these samples were analyzed by the 
+microbiological assay, which cannot distinguish analogs.Hugenschmidt et al. reported that Lactobacillus plantarum SM39 and Propionibacterium freudenreichii used in a cofermentation of whey produced up to 8 μg of cobalamin per mL (Hugenschmidt et al., 2011). Watanabe et al. (2014) reported that the addition of Propionibacteria to cabbage during sauerkraut production resulted in higher concentrations of B12 (7.2 μg/100 mL). Although we produced less vitamin B12 than their fermentations, our samples do not have the pungent odor from propionic acid.In this work cofermentation of glycerol and fructose was also confirmed to have a positive effect on the production of vitamin B12 (Table 1). Glycerol is a vital interesting topic not only for vitamin B12 production but also for the growth of cells. Glycerol works as an inducer of vitamin B12 synthesis cluster (Roth et al., 1996). In Fig. 1, cobT and cbiA genes were obviously induced by glycerol, but cbiA was induced more than cobT. The increase expression of both enzymes accelerated the synthesis of vitamin B12 and led to a higher production of vitamin B12. In this condition, vitamin B12 synthesis also increased the production of vitamin B12 analogs.Vitamin B12 dependent enzymes in L. reuteri are involved in the conversion from glycerol to 3-HPA in order to regenerate NAD+
+ with more ATP generation. Some researchers demonstrated that glycerol 
+serves only as an external hydrogen acceptor in the glycerol 
+fermentation of L. reuteri, and does not work as a carbon source ( Sriramulu et al., 2008). Our work of glycerol used as an external hydrogen acceptor (Table 2) is in agreement with the above results. An obvious shift of end products from ethanol to acetate was observed in our results (Table 2). Similar results were found in the work of Lüthi-Peng et al. (2002)
+ and coworkers. They stated that a sufficient supplementation of glucose
+ compared to glycerol could improve the generation of 1, 3-propanediol 
+and acetate, and reduced the accumulation of 3-HPA and lactate. Vitamin B12 production (Table 1)
+ was indeed improved with the supplementation of glycerol since glucose 
+was utilized via a more efficient pathway to generate ATP and glucose 
+was not involved in the redox balance, but high concentrations of 
+glycerol supplementations in our work definitely inhibited the growth of
+ cells. It may attribute to an activity of glycerol dehydratase 
+inhibited by a quorum sensing of reuterin (Bauer et al., 2010).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt
new file mode 100644
index 00000000..60d0cc37
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-000.txt
@@ -0,0 +1 @@
+Staphylococcus aureus inhibition was higher when Lactococcus garvieae produces hydrogen peroxide (H2O2).
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt
new file mode 100644
index 00000000..757e6617
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-001.txt
@@ -0,0 +1,4 @@
+Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus
+ SA15 dairy strain and the MW2 human pathogenic strain, to this growth 
+inhibition were investigated in Brain-Heart Infusion broth under a high 
+or a low aeration level.
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1 b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.a1
new file mode 100644
index 00000000..e69de29b
diff --git a/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt
new file mode 100644
index 00000000..b93370c6
--- /dev/null
+++ b/corpora/BioNLP-OST-2019/batch/BB19-rel+ner/bionlp-st/BB-rel+ner-F-26187841-002.txt
@@ -0,0 +1 @@
+Among these LAB, Lactococcus garvieae, commonly found in dairy products, can inhibit S. aureus growth in broth, milk, and cheese made from raw or pasteurized milk ( Alomar et al., 2008a, Alomar et al., 2008b and Delbes-Paus et al., 2010).
diff --git a/plans/entities.plan b/plans/entities.plan
index 3a9ec07d..80138040 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -2,193 +2,208 @@
 
 <alvisnlp-plan id="entities">
 
+  <param name="format">
+    <alias module="read" param="select"/>
+  </param>
+  
   <param name="input">
-  <alias module="read" param="sourcePath"/>
+    <alias module="read.pubmed" param="sourcePath"/>
+  </param>
+  
+  <param name="input-dir">
+    <alias module="read.bionlp-st" param="textDir"/>
   </param>
 
   <param name="input-xslt">
-  <alias module="read" param="xslTransform"/>
+    <alias module="read.pubmed" param="xslTransform"/>
   </param>
 
   <param name="outputDir">
-  <alias module="output.doc-mesh" param="outDir"/>
-  <alias module="output.taxa" param="outDir"/>
-  <alias module="output.microorganisms" param="outDir"/>
-  <alias module="output.microorganisms-short" param="outDir"/>
-  <alias module="output.bacteria" param="outDir"/>
-  <alias module="output.habitats" param="outDir"/>
-  <alias module="output.phenotypes" param="outDir"/>
-  <alias module="output.uses" param="outDir"/>
-  <alias module="output.geo" param="outDir"/>
-  <alias module="output.relations" param="outDir"/>
-  <alias module="output.relations-pheno" param="outDir"/>
-  <alias module="output.relations-use" param="outDir"/>
-  <alias module="output.dependencies.sentences" param="outDir"/>
-  <alias module="output.dependencies.anaphora" param="outDir"/>
-  <alias module="output.dependencies.dependencies" param="outDir"/>
-  <alias module="words" param="outDir"/>
-  <alias module="success" param="outDir"/>
+    <alias module="output.doc-mesh" param="outDir"/>
+    <alias module="output.taxa" param="outDir"/>
+    <alias module="output.microorganisms" param="outDir"/>
+    <alias module="output.microorganisms-short" param="outDir"/>
+    <alias module="output.bacteria" param="outDir"/>
+    <alias module="output.habitats" param="outDir"/>
+    <alias module="output.phenotypes" param="outDir"/>
+    <alias module="output.uses" param="outDir"/>
+    <alias module="output.geo" param="outDir"/>
+    <alias module="output.relations" param="outDir"/>
+    <alias module="output.relations-pheno" param="outDir"/>
+    <alias module="output.relations-use" param="outDir"/>
+    <alias module="output.dependencies.sentences" param="outDir"/>
+    <alias module="output.dependencies.anaphora" param="outDir"/>
+    <alias module="output.dependencies.dependencies" param="outDir"/>
+    <alias module="words" param="outDir"/>
+    <alias module="success" param="outDir"/>
   </param>
 
   <param name="doc-mesh">
-  <alias module="output.doc-mesh" param="fileName"/>
+    <alias module="output.doc-mesh" param="fileName"/>
   </param>
 
   <param name="taxa">
-  <alias module="output.taxa" param="fileName"/>
+    <alias module="output.taxa" param="fileName"/>
   </param>
 
   <param name="microorganisms">
-  <alias module="output.microorganisms" param="fileName"/>
+    <alias module="output.microorganisms" param="fileName"/>
   </param>
 
   <param name="microorganisms-short">
-  <alias module="output.microorganisms-short" param="fileName"/>
+    <alias module="output.microorganisms-short" param="fileName"/>
   </param>
 
   <param name="bacteria">
-  <alias module="output.bacteria" param="fileName"/>
+    <alias module="output.bacteria" param="fileName"/>
   </param>
 
-   <param name="habitats">
-  <alias module="output.habitats" param="fileName"/>
-   </param>
+  <param name="habitats">
+    <alias module="output.habitats" param="fileName"/>
+  </param>
 
   <param name="phenotypes">
-  <alias module="output.phenotypes" param="fileName"/>
+    <alias module="output.phenotypes" param="fileName"/>
   </param>
 
-	<param name="uses">
-	  <alias module="output.uses" param="fileName"/>
-	</param>
-
-	<param name="geo">
-	  <alias module="output.geo" param="fileName"/>
-	</param>
-
-	<param name="relations">
-	  <alias module="output.relations" param="fileName"/>
-	</param>
-
-	<param name="relations-pheno">
-	  <alias module="output.relations-pheno" param="fileName"/>
-	</param>
-
-	<param name="relations-use">
-	  <alias module="output.relations-use" param="fileName"/>
-	</param>
-
-	<param name="sentences">
-	  <alias module="output.dependencies.sentences" param="fileName"/>
-	</param>
-
-	<param name="anaphora">
-	  <alias module="output.dependencies.anaphora" param="fileName"/>
-	</param>
-
-	<param name="dependencies">
-	  <alias module="output.dependencies.dependencies" param="fileName"/>
-	</param>
+  <param name="uses">
+    <alias module="output.uses" param="fileName"/>
+  </param>
+  
+  <param name="geo">
+    <alias module="output.geo" param="fileName"/>
+  </param>
+  
+  <param name="relations">
+    <alias module="output.relations" param="fileName"/>
+  </param>
 
-	<param name="words">
-	  <alias module="words" param="fileName"/>
-	</param>
+  <param name="relations-pheno">
+    <alias module="output.relations-pheno" param="fileName"/>
+  </param>
 
+  <param name="relations-use">
+    <alias module="output.relations-use" param="fileName"/>
+  </param>
+  
+  <param name="sentences">
+    <alias module="output.dependencies.sentences" param="fileName"/>
+  </param>
+  
+  <param name="anaphora">
+    <alias module="output.dependencies.anaphora" param="fileName"/>
+  </param>
+  
+  <param name="dependencies">
+    <alias module="output.dependencies.dependencies" param="fileName"/>
+  </param>
+  
+  <param name="words">
+    <alias module="words" param="fileName"/>
+  </param>
+  
   <param name="success">
-  <alias module="success" param="fileName"/>
+    <alias module="success" param="fileName"/>
   </param>
 
- <param name="2017MeshTree">
-  <alias module="mesh-path" param="mappingFile"/>
+  <param name="2017MeshTree">
+    <alias module="mesh-path" param="mappingFile"/>
   </param>
 
- <param name="stopwords_EN">
-  <alias module="stopwordsprojector" param="dictFile"/>
+  <param name="stopwords_EN">
+    <alias module="stopwordsprojector" param="dictFile"/>
   </param>
 
- <param name="microorganism_stopwords">
-  <alias module="stopwordsprojector-microorganism" param="dictFile"/>
+  <param name="microorganism_stopwords">
+    <alias module="stopwordsprojector-microorganism" param="dictFile"/>
   </param>
 
- <param name="food-process-lexicon">
-  <alias module="dict" param="dictFile"/>
+  <param name="food-process-lexicon">
+    <alias module="dict" param="dictFile"/>
   </param>
 
- <!--param name="noun_adj_and_spelling_variants">
-  <alias module="term-extraction.variant-projection" param="dictFile"/>
-  </param-->
+  <!--param name="noun_adj_and_spelling_variants">
+      <alias module="term-extraction.variant-projection" param="dictFile"/>
+      </param-->
 
   <param name="taxid_microorganisms">
-  <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
-  <alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
+    <alias module="taxa.microorganisms.taxids" param="mappingFile"/>
+    <alias module="microorganisms-after-strains.taxids" param="mappingFile"/>
   </param>
 
   <param name="taxa+id_full">
-  <alias module="taxa.dict" param="dictFile"/>
+    <alias module="taxa.dict" param="dictFile"/>
   </param>
 
 
   <param name="NCBI_taxa_ontobiotope">
-   <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
+    <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
   </param>
 
 
-<!-- habitats-->
-   <param name="ontobiotope-habitat">
-   <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-on-variants.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
-   <alias module="habitats.tomap-habitats.concept-path" param="oboFiles"/> 
+  <!-- habitats-->
+  <param name="ontobiotope-habitat">
+    <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-on-variants.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
+    <alias module="habitats.tomap-habitats.concept-path" param="oboFiles"/> 
   </param>
 
   <param name="ontobiotope-tomap-habitat">
-   <alias module="habitats.tomap-habitats.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="tomapClassifier"/>
-   <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="tomapClassifier"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
   </param>
 
-<!-- phenotypes-->
-   <param name="ontobiotope-phenotypes">
-   <alias module="tomap-phenotypes.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-on-variants.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
-   <alias module="tomap-phenotypes.concept-path" param="oboFiles"/> 
+  <!-- phenotypes-->
+  <param name="ontobiotope-phenotypes">
+    <alias module="tomap-phenotypes.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-on-variants.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.concept-names" param="oboFiles"/>
+    <alias module="tomap-phenotypes.concept-path" param="oboFiles"/> 
   </param>
 
   <param name="ontobiotope-tomap-phenotypes">
-   <alias module="tomap-phenotypes.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="tomapClassifier"/>
-   <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="tomapClassifier"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="tomapClassifier"/>
   </param>
 
-<!-- use-->
-   <param name="ontobiotope-use">
-   <alias module="use.exact-match" param="oboFiles"/>
-   <alias module="use.exact-match-2" param="oboFiles"/>
+  <!-- use-->
+  <param name="ontobiotope-use">
+    <alias module="use.exact-match" param="oboFiles"/>
+    <alias module="use.exact-match-2" param="oboFiles"/>
   </param>
 
-<!-- mono anaphora-->
-   <param name="anaphoraLexicon">
-   <alias module="anaphora.anaphora-plan.coreferences.mono-anaphora.anaphora" param="dictFile"/>
+  <!-- mono anaphora-->
+  <param name="anaphoraLexicon">
+    <alias module="anaphora.anaphora-plan.coreferences.mono-anaphora.anaphora" param="dictFile"/>
   </param>
 
-<!-- multi anaphora-->
-   <param name="biAnaphoraLexicon">
-   <alias module="anaphora.anaphora-plan.coreferences.multi-ante-anaphora.bi-anaphora" param="dictFile"/>
+  <!-- multi anaphora-->
+  <param name="biAnaphoraLexicon">
+    <alias module="anaphora.anaphora-plan.coreferences.multi-ante-anaphora.bi-anaphora" param="dictFile"/>
   </param>
 
-
-  <read class="XMLReader">
-    <sourcePath>corpora/&corpus;/batch/&batch;/batch.xml</sourcePath>
-    <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
+  <read>
+    <pubmed class="XMLReader">
+      <sourcePath>corpora/&corpus;/batch/&batch;/batch.xml</sourcePath>
+      <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
+    </pubmed>
+
+    <bionlp-st class="BioNLPSTReader">
+      <active>true</active>
+      <sectionName>abstract</sectionName>
+      <textDir>corpora/&corpus;/batch/&batch;/bionlp-st</textDir>
+    </bionlp-st>
   </read>
 
   <assert class="Assert">
@@ -210,7 +225,7 @@
     <setFeatures/>
   </set-url>
 
-<!-- Get year -->
+  <!-- Get year -->
   <set-year class="Action">
     <target>documents[@year == "" and not @date == ""]</target>
     <action>set:feat:year(str:seds(@date,"^(\\d+) .+$","$1"))</action>
@@ -220,22 +235,22 @@
   <taxa file="plans/taxa.plan"/>
 
 
-<!-- Project stopwords -->
-<stopwordsprojector class="TabularProjector">
-  <dictFile>ancillaries/stopwords_EN.txt</dictFile>
-  <targetLayerName>stopwords</targetLayerName>
-  <valueFeatures>stopwords</valueFeatures>
-  <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
-  <caseInsensitive>true</caseInsensitive>
-</stopwordsprojector>
+  <!-- Project stopwords -->
+  <stopwordsprojector class="TabularProjector">
+    <dictFile>ancillaries/stopwords_EN.txt</dictFile>
+    <targetLayerName>stopwords</targetLayerName>
+    <valueFeatures>stopwords</valueFeatures>
+    <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
+    <caseInsensitive>true</caseInsensitive>
+  </stopwordsprojector>
 
-<stopwordsprojector-microorganism class="TabularProjector">
-  <dictFile>ancillaries/microorganism_stopwords.txt</dictFile>
-  <targetLayerName>microorganism-stopwords</targetLayerName>
-  <valueFeatures>stopwords</valueFeatures>
-  <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
-  <caseInsensitive>true</caseInsensitive>
-</stopwordsprojector-microorganism>
+  <stopwordsprojector-microorganism class="TabularProjector">
+    <dictFile>ancillaries/microorganism_stopwords.txt</dictFile>
+    <targetLayerName>microorganism-stopwords</targetLayerName>
+    <valueFeatures>stopwords</valueFeatures>
+    <constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
+    <caseInsensitive>true</caseInsensitive>
+  </stopwordsprojector-microorganism>
 
   <geo>
     <stanford class="StanfordNER">
@@ -323,9 +338,9 @@
   <!-- Detect abbreviations -->
   <abbrev class="Ab3P">
     <!--installDir>/projet/maiage/save/textemig/projet-work/software/Ab3P-v1.5</installDir-->
-	<!-- layers: 'short-forms', 'long-forms' -->
-	<!-- in 'short-forms', feature 'long-form' -->
-	<!-- relations: 'abbreviations', roles 'short-form', 'long-form' -->
+    <!-- layers: 'short-forms', 'long-forms' -->
+    <!-- in 'short-forms', feature 'long-form' -->
+    <!-- relations: 'abbreviations', roles 'short-form', 'long-form' -->
   </abbrev>
 
   <!-- Project process lexicon -->
@@ -451,41 +466,41 @@
   <!-- Tag and normalize Use entities -->
   <use file="plans/use-extraction.plan"/>
 
-<!-- Filter entities spanning stopwords -->
-<stopwords class="Action">
-  <target>documents.sections.layer:habitats[span:stopwords] | documents.sections.layer:Geographical[span:stopwords] | documents.sections.layer:locations[span:stopwords] | documents.sections.layer:microorganism[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:bacteria[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:phenotypes[span:stopwords] | documents.sections.layer:uses[span:stopwords]</target>
-  <action>delete</action>
-  <deleteElements/>
-</stopwords>
-
- <!-- <module id="remove-microorganism-equal-to-numbers-1" class="Action"> -->
- <!--    <target>documents.sections.layer:microorganism[@form =~ "^\\d+$"]</target> -->
- <!--    <action>set:feat:to-remove(not section.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^\\d+$"])</action> -->
- <!--    <setFeatures/> -->
- <!--  </module> -->
- <!-- <module id="remove-microorganism-equal-to-numbers-2" class="Action"> -->
- <!--    <target>documents.sections.layer:microorganism[@to-remove == "true"]</target> -->
- <!--    <action>remove:microorganism</action> -->
- <!--    <removeFromLayer/> -->
- <!--  </module> -->
- <remove-short-microorganism-1 class="Action">
+  <!-- Filter entities spanning stopwords -->
+  <stopwords class="Action">
+    <target>documents.sections.layer:habitats[span:stopwords] | documents.sections.layer:Geographical[span:stopwords] | documents.sections.layer:locations[span:stopwords] | documents.sections.layer:microorganism[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:bacteria[span:stopwords or span:microorganism-stopwords] | documents.sections.layer:phenotypes[span:stopwords] | documents.sections.layer:uses[span:stopwords]</target>
+    <action>delete</action>
+    <deleteElements/>
+  </stopwords>
+
+  <!-- <module id="remove-microorganism-equal-to-numbers-1" class="Action"> -->
+  <!--    <target>documents.sections.layer:microorganism[@form =~ "^\\d+$"]</target> -->
+  <!--    <action>set:feat:to-remove(not section.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^\\d+$"])</action> -->
+  <!--    <setFeatures/> -->
+  <!--  </module> -->
+  <!-- <module id="remove-microorganism-equal-to-numbers-2" class="Action"> -->
+  <!--    <target>documents.sections.layer:microorganism[@to-remove == "true"]</target> -->
+  <!--    <action>remove:microorganism</action> -->
+  <!--    <removeFromLayer/> -->
+  <!--  </module> -->
+  <remove-short-microorganism-1 class="Action">
     <target>documents.sections.layer:microorganism[@form =~ "^..?$"]</target>
     <action>set:feat:to-remove(not section.document.sections.layer:microorganism[@canonical-name == target.@canonical-name and not @form =~ "^..?$"])</action>
     <setFeatures/>
   </remove-short-microorganism-1>
- <remove-short-microorganism-2 class="Action">
+  <remove-short-microorganism-2 class="Action">
     <target>documents.sections.layer:microorganism[@to-remove == "true"]</target>
     <action>remove:microorganism</action>
     <removeFromLayer/>
   </remove-short-microorganism-2>
 
- <remove-microorganism-spanning-units class="Action">
+  <remove-microorganism-spanning-units class="Action">
     <target>documents.sections.layer:microorganism[outside:units]</target>
     <action>remove:microorganism</action>
     <removeFromLayer/>
- </remove-microorganism-spanning-units>
+  </remove-microorganism-spanning-units>
 
-<!-- Get lemmatized form -->
+  <!-- Get lemmatized form -->
   <get-CD-lemmas class="Action">
     <target>documents.sections.layer:words[@lemma == "@card@"]</target>
     <action>set:feat:lemma(@form)</action>
@@ -504,13 +519,13 @@
   </get-lemmas-for-entities-2>
 
   <!--
-  <module id="mbto-vocabulary" class="FileMapper">
-    <target>documents.sections.layer:words</target>
-    <form>@lemma</form>
-    <ignoreCase/>
-    <mappingFile>&ontobiotope;_words.txt</mappingFile>
-    <targetFeatures>mbto-word</targetFeatures>
-  </module>
+      <module id="mbto-vocabulary" class="FileMapper">
+      <target>documents.sections.layer:words</target>
+      <form>@lemma</form>
+      <ignoreCase/>
+      <mappingFile>&ontobiotope;_words.txt</mappingFile>
+      <targetFeatures>mbto-word</targetFeatures>
+      </module>
   -->
 
   <anaphora>
@@ -526,37 +541,37 @@
     <!-- XXX foodborne, soilborne, all water and soil -->
     <localization-relations>
       <triggers class="Action">
-    	<target>documents.sections.layer:words[@form =~ "^(parasit|attack|coloniz|flora|infect|inhabit|invade|important|host|environment|niche|habitat|effect|contamin|ecolog|toward|presen|subject|induce|implicate|ingest|grow|detect|found|live|spread|survive|unable|commensal|isolate|symbio|relationship|present|discover|observ|econom|disease|virulence|chronic|symptom|syndrome|severe|fever|caus|treat|prevalence|outbreak|epidem|ill|pathogen|phytopathogen|infest|ingest|fed|eat)"]</target>
-    	<action>add:triggers</action>
-    	<addToLayer/>
+	<target>documents.sections.layer:words[@form =~ "^(parasit|attack|coloniz|flora|infect|inhabit|invade|important|host|environment|niche|habitat|effect|contamin|ecolog|toward|presen|subject|induce|implicate|ingest|grow|detect|found|live|spread|survive|unable|commensal|isolate|symbio|relationship|present|discover|observ|econom|disease|virulence|chronic|symptom|syndrome|severe|fever|caus|treat|prevalence|outbreak|epidem|ill|pathogen|phytopathogen|infest|ingest|fed|eat)"]</target>
+	<action>add:triggers</action>
+	<addToLayer/>
       </triggers>
 
       <create-relation class="Action">
-    	<target>documents.sections</target>
-    	<action>new:relation:CooccurrenceLocalization</action>
-    	<createRelations/>
+	<target>documents.sections</target>
+	<action>new:relation:CooccurrenceLocalization</action>
+	<createRelations/>
       </create-relation>
 
       <create-tuples class="Action">
-      	<target>documents.sections.layer:sentences[inside:triggers]</target>
-      	<action>
-      	  inside:microorganism as b.
-      	  target.inside:locations as l.
-      	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
-      	</action>
-      	<createTuples/>
-      	<setArguments/>
+	<target>documents.sections.layer:sentences[inside:triggers]</target>
+	<action>
+	  inside:microorganism as b.
+	  target.inside:locations as l.
+	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
+	</action>
+	<createTuples/>
+	<setArguments/>
       </create-tuples>
 
       <create-tuples-anaphora class="Action">
-  	<target>documents.sections.layer:sentences[inside:triggers and not inside:microorganism]</target>
-  	<action>
-  	  inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as b.
-  	  target.inside:locations as l.
-  	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
-  	</action>
-  	<createTuples/>
-  	<setArguments/>
+	<target>documents.sections.layer:sentences[inside:triggers and not inside:microorganism]</target>
+	<action>
+	  inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as b.
+	  target.inside:locations as l.
+	  section.relations:CooccurrenceLocalization.new:tuple.(set:arg:Bacterium(b)|set:arg:Localization(l))
+	</action>
+	<createTuples/>
+	<setArguments/>
       </create-tuples-anaphora>
     </localization-relations>
   </predictions>
@@ -567,37 +582,37 @@
     <deleteElements/>
   </remove-geographical-relations>
 
-<phenotype-relations>
-  <find-pattern class="PatternMatcher">
-    <pattern>
-      [outside:phenotypes]+
-      [true]{0,4}
-      ([outside:microorganism or @microorganism]+
-      [@form==","]?)+
-      ([@form=="and"]
-      [outside:microorganism or @microorganism])?
-    </pattern>
-    <actions>
-      <createAnnotation layer="phenotype-relations"/>
-    </actions>
-  </find-pattern>
-
-  <create-relation class="Action">
-    <target>documents.sections</target>
-    <action>new:relation:PhenotypeRelation</action>
-    <createRelations/>
-  </create-relation>
-
-  <create-tuple class="Action">
-    <target>documents.sections.layer:phenotype-relations[outside:sentences]</target>
-    <action>
-      target.inside:phenotypes as p.
-      target.inside:microorganism as m.
-      section.relations:PhenotypeRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Phenotype(p))
-    </action>
-    <createTuples/>
-    <setArguments/>
-  </create-tuple>
+  <phenotype-relations>
+    <find-pattern class="PatternMatcher">
+      <pattern>
+	[outside:phenotypes]+
+	[true]{0,4}
+	([outside:microorganism or @microorganism]+
+	[@form==","]?)+
+	([@form=="and"]
+	[outside:microorganism or @microorganism])?
+      </pattern>
+      <actions>
+	<createAnnotation layer="phenotype-relations"/>
+      </actions>
+    </find-pattern>
+
+    <create-relation class="Action">
+      <target>documents.sections</target>
+      <action>new:relation:PhenotypeRelation</action>
+      <createRelations/>
+    </create-relation>
+
+    <create-tuple class="Action">
+      <target>documents.sections.layer:phenotype-relations[outside:sentences]</target>
+      <action>
+	target.inside:phenotypes as p.
+	target.inside:microorganism as m.
+	section.relations:PhenotypeRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Phenotype(p))
+      </action>
+      <createTuples/>
+      <setArguments/>
+    </create-tuple>
 
     <!-- <create-tuple class="Action"> -->
     <!--   <target>documents.sections.layer:sentences</target> -->
@@ -621,15 +636,15 @@
     <!--   <setArguments/> -->
     <!-- </module> -->
 
-</phenotype-relations>
+  </phenotype-relations>
 
-<use-relations>
+  <use-relations>
 
-  <create-relation class="Action">
-    <target>documents.sections</target>
-    <action>new:relation:UseRelation</action>
-    <createRelations/>
-  </create-relation>
+    <create-relation class="Action">
+      <target>documents.sections</target>
+      <action>new:relation:UseRelation</action>
+      <createRelations/>
+    </create-relation>
 
     <create-tuple class="Action">
       <target>documents.sections.layer:sentences</target>
@@ -645,15 +660,15 @@
     <create-tuples-anaphora class="Action">
       <target>documents.sections.layer:sentences[not inside:microorganism]</target>
       <action>
-  	inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as m.
-  	target.inside:uses as p.
-  	section.relations:UseRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Use(p))
+	inside:anaphora.tuples:coreferences:Anaphora.(args:Ante|args:AnteTwo) as m.
+	target.inside:uses as p.
+	section.relations:UseRelation.new:tuple.(set:arg:Microorganism(m)|set:arg:Use(p))
       </action>
       <createTuples/>
       <setArguments/>
     </create-tuples-anaphora>
 
-</use-relations>
+  </use-relations>
 
   <output>
     <doc-mesh class="TabularExport">
@@ -676,16 +691,16 @@
       <fileName>"taxa.txt"</fileName>
       <lines>documents.sections.layer:taxa</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </taxa>
 
@@ -695,16 +710,16 @@
       <fileName>"microorganisms.txt"</fileName>
       <lines>documents.sections.layer:microorganism</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </microorganisms>
 
@@ -714,16 +729,16 @@
       <fileName>"microorganisms-short.txt"</fileName>
       <lines>documents.sections.layer:microorganism[outside:words and not @form == outside:words.@form]</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </microorganisms-short>
 
@@ -733,16 +748,16 @@
       <fileName>"bacteria.txt"</fileName>
       <lines>documents.sections.layer:bacteria</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@taxid;
-    	@canonical-name;
-    	@path;
-    	@rank
+	@taxid;
+	@canonical-name;
+	@path;
+	@rank
       </columns>
     </bacteria>
 
@@ -752,18 +767,18 @@
       <fileName>"habitats.txt"</fileName>
       <lines>documents.sections.layer:habitats</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </habitats>
 
@@ -773,18 +788,18 @@
       <fileName>"phenotypes.txt"</fileName>
       <lines>documents.sections.layer:phenotypes</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </phenotypes>
 
@@ -794,18 +809,18 @@
       <fileName>"uses.txt"</fileName>
       <lines>documents.sections.layer:uses</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string;
-    	@concept-id;
-    	@concept-name;
-    	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
-    	@explain_concept-synonym;
-    	@explain_significant-head;
-    	@score
+	@concept-id;
+	@concept-name;
+	str:join:','(sort:nsval(nav:features:concept-path,@value),@value);
+	@explain_concept-synonym;
+	@explain_significant-head;
+	@score
       </columns>
     </uses>
 
@@ -815,11 +830,11 @@
       <fileName>"geo.txt"</fileName>
       <lines>documents.sections.layer:Geographical</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	start ^ "-" ^ end;
-    	@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	start ^ "-" ^ end;
+	@form;
 	@lemma-string
       </columns>
     </geo>
@@ -830,20 +845,20 @@
       <fileName>"relations.txt"</fileName>
       <lines>documents.sections.relations:CooccurrenceLocalization.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Bacterium.@taxid;
-    	args:Bacterium.@form;
-    	args:Bacterium.@lemma-string;
-    	args:Bacterium.@canonical-name;
-    	args:Bacterium.@path;
-    	args:Localization.@concept-id;
-    	args:Localization.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Bacterium.@taxid;
+	args:Bacterium.@form;
+	args:Bacterium.@lemma-string;
+	args:Bacterium.@canonical-name;
+	args:Bacterium.@path;
+	args:Localization.@concept-id;
+	args:Localization.@form;
 	args:Localization.@lemma-string;
-    	args:Localization.@concept-name;
+	args:Localization.@concept-name;
 	str:join:','(sort:nsval(args:Localization.nav:features:concept-path,@value),@value)
-    	<!-- args:Localization.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Localization.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations>
 
@@ -853,20 +868,20 @@
       <fileName>"phenotype-relations.txt"</fileName>
       <lines>documents.sections.relations:PhenotypeRelation.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Microorganism.@taxid;
-    	args:Microorganism.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Microorganism.@taxid;
+	args:Microorganism.@form;
 	args:Microorganism.@lemma-string;
-    	args:Microorganism.@canonical-name;
-    	args:Microorganism.@path;
-    	args:Phenotype.@concept-id;
-    	args:Phenotype.@form;
+	args:Microorganism.@canonical-name;
+	args:Microorganism.@path;
+	args:Phenotype.@concept-id;
+	args:Phenotype.@form;
 	args:Phenotype.@lemma-string;
-    	args:Phenotype.@concept-name;
+	args:Phenotype.@concept-name;
 	str:join:','(sort:nsval(args:Phenotype.nav:features:concept-path,@value),@value)
-    	<!-- args:Phenotype.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Phenotype.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations-pheno>
 
@@ -876,20 +891,20 @@
       <fileName>"uses-relations.txt"</fileName>
       <lines>documents.sections.relations:UseRelation.tuples</lines>
       <columns separator=";">
-    	"&batch;";
-    	section.document.@id;
-    	section.@name;
-    	args:Microorganism.@taxid;
-    	args:Microorganism.@form;
+	"&batch;";
+	section.document.@id;
+	section.@name;
+	args:Microorganism.@taxid;
+	args:Microorganism.@form;
 	args:Microorganism.@lemma-string;
-    	args:Microorganism.@canonical-name;
-    	args:Microorganism.@path;
-    	args:Use.@concept-id;
-    	args:Use.@form;
+	args:Microorganism.@canonical-name;
+	args:Microorganism.@path;
+	args:Use.@concept-id;
+	args:Use.@form;
 	args:Use.@lemma-string;
-    	args:Use.@concept-name;
+	args:Use.@concept-name;
 	str:join:','(sort:nsval(args:Use.nav:features:concept-path,@value),@value)
-    	<!-- args:Use.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
+	<!-- args:Use.str:join:','(sort:nsval(nav:features:concept-path,@value),@value) -->
       </columns>
     </relations-use>
 
@@ -912,7 +927,7 @@
     <!-- 	| stmt:res(obta:document, pmid^section.document.@id) -->
     <!-- 	| stmt:str(obta:form, @form) -->
     <!-- 	); -->
-	
+    
     <!-- 	documents.sections.layer[@concept-id].( -->
     <!-- 	  stmt:res(rdf:type, OBT^str:after:':'(@concept-id)) -->
     <!-- 	| stmt:res(obta:document, pmid^section.document.@id) -->
@@ -925,12 +940,12 @@
     <!-- </rdf> -->
 
     <!--
-    <module id="document-richness" class="TabularExport">
-      <outDir>corpora/&corpus;/batch/&batch;</outDir>
-      <files>$</files>
-      <fileName>"document-richness.txt"</fileName>
-      <lines>documents[sections[layer:microorganism and layer:habitats]]</lines>
-      <columns separator=";">
+	<module id="document-richness" class="TabularExport">
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"document-richness.txt"</fileName>
+	<lines>documents[sections[layer:microorganism and layer:habitats]]</lines>
+	<columns separator=";">
 	"&batch;";
 	@id;
 	int(sections.layer:microorganism);
@@ -941,117 +956,117 @@
 	int(sort:nsval(sections.layer:words[@mbto-word], @mbto-word));
 	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @taxid);
 	str:join:'\t'(sort:nsval(sections.layer:habitats, @concept-id), @concept-id);
- 	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @canonical-name);
+	str:join:'\t'(sort:nsval(sections.layer:microorganism, @taxid), @canonical-name);
 	str:join:'\t'(sort:nsval(sections.layer:habitats, @concept-id), @concept-name);
 	str:join:'\t'(sort:nsval(sections.layer:words[@mbto-word], @mbto-word), @mbto-word)
-     </columns>
-    </module>
+	</columns>
+	</module>
     -->
 
     <dependencies>
       <index-words class="Action">
-  	<target>documents.sections.layer:sentences[@name != "author"]</target>
-  	<action>id:enumerate:word-index(inside:words)</action>
-  	<setFeatures/>
+	<target>documents.sections.layer:sentences[@name != "author"]</target>
+	<action>id:enumerate:word-index(inside:words)</action>
+	<setFeatures/>
       </index-words>
 
       <index-sentences class="Action">
-  	<target>documents.sections[@name != "author"]</target>
-  	<action>id:enumerate:sentence-index(layer:sentences)</action>
-  	<setFeatures/>
+	<target>documents.sections[@name != "author"]</target>
+	<action>id:enumerate:sentence-index(layer:sentences)</action>
+	<setFeatures/>
       </index-sentences>
 
       <sentences class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"sentences.txt"</fileName>
-  	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
-  	<columns separator=";">
-  	  section.document.@id;
-  	  section.@name;
-  	  @sentence-index;
-  	  start ^ "-" ^ end;
-  	  str:replace(@form, "\n", " ")
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "SENTENCE",
-  	  "OFFSET",
-  	  "FORM"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"sentences.txt"</fileName>
+	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
+	<columns separator=";">
+	  section.document.@id;
+	  section.@name;
+	  @sentence-index;
+	  start ^ "-" ^ end;
+	  str:replace(@form, "\n", " ")
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "SENTENCE",
+	  "OFFSET",
+	  "FORM"
+	</headers>
       </sentences>
 
       <anaphora class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"anaphora.txt"</fileName>
-  	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
-  	<columns separator=";">
-  	  relation.section.document.@id;
-  	  relation.section.@name;
-  	  args:Anaphora.start;
-  	  args:Anaphora.outside:sentences.@sentence-index;
-  	  args:Anaphora.@form;
-  	  args:Ante.start;
-  	  args:Ante.outside:sentences.@sentence-index;
-  	  args:Ante.@form;
-  	  args:AnteTwo.start;
-  	  args:AnteTwo.outside:sentences.@sentence-index;
-  	  args:AnteTwo.@form
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "ANAPHOR OFFSET",
-  	  "ANAPHOR SENTENCE",
-  	  "ANAPHOR FORM",
-  	  "ANTE OFFSET",
-  	  "ANTE SENTENCE",
-  	  "ANTE FORM",
-  	  "ANTE 2 OFFSET",
-  	  "ANTE 2 SENTENCE",
-  	  "ANTE 2 FORM"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"anaphora.txt"</fileName>
+	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
+	<columns separator=";">
+	  relation.section.document.@id;
+	  relation.section.@name;
+	  args:Anaphora.start;
+	  args:Anaphora.outside:sentences.@sentence-index;
+	  args:Anaphora.@form;
+	  args:Ante.start;
+	  args:Ante.outside:sentences.@sentence-index;
+	  args:Ante.@form;
+	  args:AnteTwo.start;
+	  args:AnteTwo.outside:sentences.@sentence-index;
+	  args:AnteTwo.@form
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "ANAPHOR OFFSET",
+	  "ANAPHOR SENTENCE",
+	  "ANAPHOR FORM",
+	  "ANTE OFFSET",
+	  "ANTE SENTENCE",
+	  "ANTE FORM",
+	  "ANTE 2 OFFSET",
+	  "ANTE 2 SENTENCE",
+	  "ANTE 2 FORM"
+	</headers>
       </anaphora>
 
       <dependencies class="TabularExport">
-  	<outDir>corpora/&corpus;/batch/&batch;</outDir>
-  	<files>$</files>
-  	<fileName>"dependencies.txt"</fileName>
-  	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
-  	<columns separator=";">
-  	  relation.section.document.@id;
-  	  relation.section.@name;
-  	  args:sentence.@sentence-index;
-  	  @label;
-  	  args:head.@word-index;
-  	  args:head.@form;
-  	  args:head.@lemma;
-  	  args:head.@pos;
-  	  args:head.start ^ "-" ^ args:head.end;
-  	  args:dependent.@word-index;
-  	  args:dependent.@form;
-  	  args:dependent.@lemma;
-  	  args:dependent.@pos;
-  	  args:dependent.start ^ "-" ^ args:dependent.end
-  	</columns>
-  	<headers>
-  	  "DOCUMENT",
-  	  "SECTION",
-  	  "SENTENCE",
-  	  "LABEL",
-  	  "HEAD INDEX",
-  	  "HEAD FORM",
-  	  "HEAD LEMMA",
-  	  "HEAD POS",
-  	  "HEAD OFFSET",
-  	  "DEPENDENT INDEX",
-  	  "DEPENDENT FORM",
-  	  "DEPENDENT LEMMA",
-  	  "DEPENDENT POS",
-  	  "DEPENDENT OFFSET"
-  	</headers>
+	<outDir>corpora/&corpus;/batch/&batch;</outDir>
+	<files>$</files>
+	<fileName>"dependencies.txt"</fileName>
+	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
+	<columns separator=";">
+	  relation.section.document.@id;
+	  relation.section.@name;
+	  args:sentence.@sentence-index;
+	  @label;
+	  args:head.@word-index;
+	  args:head.@form;
+	  args:head.@lemma;
+	  args:head.@pos;
+	  args:head.start ^ "-" ^ args:head.end;
+	  args:dependent.@word-index;
+	  args:dependent.@form;
+	  args:dependent.@lemma;
+	  args:dependent.@pos;
+	  args:dependent.start ^ "-" ^ args:dependent.end
+	</columns>
+	<headers>
+	  "DOCUMENT",
+	  "SECTION",
+	  "SENTENCE",
+	  "LABEL",
+	  "HEAD INDEX",
+	  "HEAD FORM",
+	  "HEAD LEMMA",
+	  "HEAD POS",
+	  "HEAD OFFSET",
+	  "DEPENDENT INDEX",
+	  "DEPENDENT FORM",
+	  "DEPENDENT LEMMA",
+	  "DEPENDENT POS",
+	  "DEPENDENT OFFSET"
+	</headers>
       </dependencies>
     </dependencies>
   </output>
@@ -1088,7 +1103,7 @@
   <!-- 	  <deleteElements/> -->
   <!-- 	</module> -->
   <!--     </sequence> -->
-      
+  
   <!--     <module id="common" class="Action"> -->
   <!-- 	<target>documents.sections.layer:Species[span:microorganism]</target> -->
   <!-- 	<action>remove:Species|span:microorganism.set:feat:source("Common")</action> -->
@@ -1192,30 +1207,30 @@
   <!-- 	    </args> -->
   <!-- 	  </relation> -->
 
-	  <!--
-	  <text>
-	    <type>"Anaphor"</type>
-	    <instances>layer:mono-anaphora|layer:bi-anaphora</instances>
-	  </text>
-
-	  <relation>
-	    <type>"Coreference"</type>
-	    <instances>relations:coreferences.tuples[args:Ante[@bacteria == "true"]]</instances>
-	    <args>
-	      <Anaphor>args:Anaphora</Anaphor>
-	      <Antecedent>args:Ante</Antecedent>
-	    </args>
-	  </relation>
-
-	  <relation>
-	    <type>"Coreference"</type>
-	    <instances>relations:coreferences.tuples[args:AnteTwo[@bacteria == "true"]]</instances>
-	    <args>
-	      <Anaphor>args:Anaphora</Anaphor>
-	      <Antecedent>args:AnteTwo</Antecedent>
-	    </args>
-	  </relation>
-	  -->
+  <!--
+      <text>
+      <type>"Anaphor"</type>
+      <instances>layer:mono-anaphora|layer:bi-anaphora</instances>
+      </text>
+
+<relation>
+<type>"Coreference"</type>
+<instances>relations:coreferences.tuples[args:Ante[@bacteria == "true"]]</instances>
+<args>
+<Anaphor>args:Anaphora</Anaphor>
+<Antecedent>args:Ante</Antecedent>
+</args>
+</relation>
+
+<relation>
+<type>"Coreference"</type>
+<instances>relations:coreferences.tuples[args:AnteTwo[@bacteria == "true"]]</instances>
+<args>
+<Anaphor>args:Anaphora</Anaphor>
+<Antecedent>args:AnteTwo</Antecedent>
+</args>
+</relation>
+  -->
   <!-- 	</element> -->
   <!--     </annotationSets> -->
   <!--   </module> -->
@@ -1237,19 +1252,19 @@
     <index class="AlvisDBIndexer">
       <indexDir>corpora/&corpus;/batch/&batch;/adb</indexDir>
       <elements>
-  	<relations>
-  	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
-  	  <id>"&batch;_" ^ id:unique</id>
-  	  <name>"Localization"</name>
-  	  <type>"localization"</type>
-  	  <args>args:Bacterium|args:Localization</args>
-  	  <arg-id>if @taxid then @taxid else @concept-id</arg-id>
-  	  <arg-name>if @taxid then @canonical-name else @concept-name</arg-name>
-  	  <ancestors>nav:features:ancestors</ancestors>
-  	  <ancestor-id>@value</ancestor-id>
-  	  <arg-doc>section.document.@id</arg-doc>
-  	  <arg-sec>section.@name</arg-sec>
-  	</relations>
+	<relations>
+	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
+	  <id>"&batch;_" ^ id:unique</id>
+	  <name>"Localization"</name>
+	  <type>"localization"</type>
+	  <args>args:Bacterium|args:Localization</args>
+	  <arg-id>if @taxid then @taxid else @concept-id</arg-id>
+	  <arg-name>if @taxid then @canonical-name else @concept-name</arg-name>
+	  <ancestors>nav:features:ancestors</ancestors>
+	  <ancestor-id>@value</ancestor-id>
+	  <arg-doc>section.document.@id</arg-doc>
+	  <arg-sec>section.@name</arg-sec>
+	</relations>
       </elements>
     </index>
   </adb>
@@ -1266,19 +1281,19 @@
     <propertyKeys/>
     <documents>
       <fields>
-  	<instances>sections:title | sections:abstract</instances>
-  	<annotations>
-  	  <instances>layer:microorganism</instances>
-  	  <text>"{taxon}" ^ @path ^ "/"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:sentences</instances>
-  	  <text>"{SENT}"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:habitats</instances>
-  	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
-  	</annotations>
+	<instances>sections:title | sections:abstract</instances>
+	<annotations>
+	  <instances>layer:microorganism</instances>
+	  <text>"{taxon}" ^ @path ^ "/"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:sentences</instances>
+	  <text>"{SENT}"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:habitats</instances>
+	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
+	</annotations>
 	<annotations>
 	  <instances>layer:phenotypes</instances>
 	  <text>"{phenotype}" ^ @concept-path ^ "/"</text>
@@ -1287,112 +1302,112 @@
 	  <instances>layer:uses</instances>
 	  <text>"{use}" ^ @concept-path ^ "/"</text>
 	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
 
 	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
 
       </fields>
       <fields>
-  	<instances>nav:features:mesh-name</instances>
-  	<field-name>"mesh"</field-name>
-  	<keyword>@value</keyword>
+	<instances>nav:features:mesh-name</instances>
+	<field-name>"mesh"</field-name>
+	<keyword>@value</keyword>
       </fields>
       <fields>
-  	<instances>sections:author</instances>
+	<instances>sections:author</instances>
       </fields>
       <fields>
-  	<instances>sections:author</instances>
-  	<field-name>"full-author"</field-name>
-  	<keyword>contents</keyword>
+	<instances>sections:author</instances>
+	<field-name>"full-author"</field-name>
+	<keyword>contents</keyword>
       </fields>
       <fields>
-  	<instances>$</instances>
-  	<field-name>"pmid"</field-name>
-  	<keyword>@id</keyword>
+	<instances>$</instances>
+	<field-name>"pmid"</field-name>
+	<keyword>@id</keyword>
       </fields>
       <fields>
-  	<instances>$[@year]</instances>
-  	<field-name>"year"</field-name>
-  	<keyword>@year</keyword>
+	<instances>$[@year]</instances>
+	<field-name>"year"</field-name>
+	<keyword>@year</keyword>
       </fields>
       <fields>
-  	<instances>$[@journal]</instances>
-  	<field-name>"journal"</field-name>
-  	<keyword>@journal</keyword>
+	<instances>$[@journal]</instances>
+	<field-name>"journal"</field-name>
+	<keyword>@journal</keyword>
       </fields>
       <fields>
-        <instances>$[@url]</instances>
-        <field-name>"url"</field-name>
-        <keyword>document.@url</keyword>
+	<instances>$[@url]</instances>
+	<field-name>"url"</field-name>
+	<keyword>document.@url</keyword>
       </fields>
     </documents>
   </index>
 
- <index-food class="AlvisIRIndexer">
+  <index-food class="AlvisIRIndexer">
     <indexDir>corpora/&corpus;/batch/&batch;/index-food</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
@@ -1404,19 +1419,19 @@
     <propertyKeys/>
     <documents>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="title"] | sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="abstract"]</instances>
-  	<annotations>
-  	  <instances>layer:microorganism</instances>
-  	  <text>"{taxon}" ^ @path ^ "/"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:sentences</instances>
-  	  <text>"{SENT}"</text>
-  	</annotations>
-  	<annotations>
-  	  <instances>layer:habitats</instances>
-  	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
-  	</annotations>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="title"] | sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name =="abstract"]</instances>
+	<annotations>
+	  <instances>layer:microorganism</instances>
+	  <text>"{taxon}" ^ @path ^ "/"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:sentences</instances>
+	  <text>"{SENT}"</text>
+	</annotations>
+	<annotations>
+	  <instances>layer:habitats</instances>
+	  <text>"{habitat}" ^ @concept-path ^ "/"</text>
+	</annotations>
 	<annotations>
 	  <instances>layer:phenotypes</instances>
 	  <text>"{phenotype}" ^ @concept-path ^ "/"</text>
@@ -1425,148 +1440,236 @@
 	  <instances>layer:uses</instances>
 	  <text>"{use}" ^ @concept-path ^ "/"</text>
 	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:CooccurrenceLocalization.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Bacterium.id:unique</taxon>
-  	    <habitat>args:Localization.id:unique</habitat>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:PhenotypeRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <phenotype>args:Phenotype.id:unique</phenotype>
-  	  </arguments>
-  	</annotations>
 	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
-  	<annotations>
-  	  <instances>relations:UseRelation.tuples</instances>
-  	  <fragments>
-  	    <instances>sort:ival(args, start)</instances>
-  	  </fragments>
-  	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
-  	  <arguments>
-  	    <taxon>args:Microorganism.id:unique</taxon>
-  	    <use>args:Use.id:unique</use>
-  	  </arguments>
-  	</annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}{taxon}" ^ args:Bacterium.@path ^ "/~{habitat}" ^ args:Localization.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:CooccurrenceLocalization.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{livesin}" ^ args:Bacterium.@form ^ "/~" ^ args:Localization.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Bacterium.id:unique</taxon>
+	    <habitat>args:Localization.id:unique</habitat>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}{taxon}" ^ args:Microorganism.@path ^ "/~{phenotype}" ^ args:Phenotype.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:PhenotypeRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{exhibits}" ^ args:Microorganism.@form ^ "/~" ^ args:Phenotype.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <phenotype>args:Phenotype.id:unique</phenotype>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}{taxon}" ^ args:Microorganism.@path ^ "/~{use}" ^ args:Use.@concept-path ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
+	<annotations>
+	  <instances>relations:UseRelation.tuples</instances>
+	  <fragments>
+	    <instances>sort:ival(args, start)</instances>
+	  </fragments>
+	  <text>"{studiedfor}" ^ args:Microorganism.@form ^ "/~" ^ args:Use.@form ^ "/"</text>
+	  <arguments>
+	    <taxon>args:Microorganism.id:unique</taxon>
+	    <use>args:Use.id:unique</use>
+	  </arguments>
+	</annotations>
       </fields>
       <fields>
-  	<instances>nav:features:mesh-name</instances>
-  	<field-name>"mesh"</field-name>
-  	<keyword>@value</keyword>
+	<instances>nav:features:mesh-name</instances>
+	<field-name>"mesh"</field-name>
+	<keyword>@value</keyword>
       </fields>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
       </fields>
       <fields>
-  	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
-  	<field-name>"full-author"</field-name>
-  	<keyword>contents</keyword>
+	<instances>sections[document.@id in "corpora/&corpus;/food-pmids.txt" and @name == "author"]</instances>
+	<field-name>"full-author"</field-name>
+	<keyword>contents</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt"]</instances>
-  	<field-name>"pmid"</field-name>
-  	<keyword>@id</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt"]</instances>
+	<field-name>"pmid"</field-name>
+	<keyword>@id</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @year]</instances>
-  	<field-name>"year"</field-name>
-  	<keyword>@year</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @year]</instances>
+	<field-name>"year"</field-name>
+	<keyword>@year</keyword>
       </fields>
       <fields>
-  	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @journal]</instances>
-  	<field-name>"journal"</field-name>
-  	<keyword>@journal</keyword>
+	<instances>$[@id in "corpora/&corpus;/food-pmids.txt" and @journal]</instances>
+	<field-name>"journal"</field-name>
+	<keyword>@journal</keyword>
       </fields>
       <fields>
-        <instances>$[@url]</instances>
-        <field-name>"url"</field-name>
-        <keyword>document.@url</keyword>
+	<instances>$[@url]</instances>
+	<field-name>"url"</field-name>
+	<keyword>document.@url</keyword>
       </fields>
     </documents>
   </index-food>
 
-<!-- HTML visualization -->
-<add-feature class="Action">
-  <target>documents.sections.layer:habitats</target>
-  <action>set:feat:ne-type("Habitat")</action>
-  <setFeatures/>
-</add-feature>
-<!-- <module id="add-feature0" class="Action"> -->
-<!--   <target>documents.sections.layer:habitats</target> -->
-<!--   <action>set:feat:before(target.overlapping:words{0}.@form)</action> -->
-<!--   <setFeatures/> -->
-<!-- </module> -->
-<add-feature2 class="Action">
-  <target>documents.sections.layer:phenotypes</target>
-  <action>set:feat:ne-type("Phenotype")</action>
-  <setFeatures/>
-</add-feature2>
-<add-feature3 class="Action">
-  <target>documents.sections.layer:microorganism</target>
-  <action>set:feat:ne-type("Microorganism")</action>
-  <setFeatures/>
-</add-feature3>
-<html class="QuickHTML">
-  <active>false</active>
-  <outDir>corpora/&corpus;/batch/&batch;/html</outDir>
-  <classFeature>ne-type</classFeature>
-  <layers>phenotypes,microorganism,habitats</layers>
-  <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
-</html>
-
-<words class="TabularExport">
-  <outDir>corpora/&corpus;/batch/&batch;</outDir>
-  <files>$</files>
-  <fileName>"words.txt"</fileName>
-  <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
-  <columns separator=";">
-    section.document.@id;
-    @form
-  </columns>
-</words>
+  <!-- HTML visualization -->
+  <add-feature class="Action">
+    <target>documents.sections.layer:habitats</target>
+    <action>set:feat:ne-type("Habitat")</action>
+    <setFeatures/>
+  </add-feature>
+  <!-- <module id="add-feature0" class="Action"> -->
+  <!--   <target>documents.sections.layer:habitats</target> -->
+  <!--   <action>set:feat:before(target.overlapping:words{0}.@form)</action> -->
+  <!--   <setFeatures/> -->
+  <!-- </module> -->
+  <add-feature2 class="Action">
+    <target>documents.sections.layer:phenotypes</target>
+    <action>set:feat:ne-type("Phenotype")</action>
+    <setFeatures/>
+  </add-feature2>
+  <add-feature3 class="Action">
+    <target>documents.sections.layer:microorganism</target>
+    <action>set:feat:ne-type("Microorganism")</action>
+    <setFeatures/>
+  </add-feature3>
+  <html class="QuickHTML">
+    <active>false</active>
+    <outDir>corpora/&corpus;/batch/&batch;/html</outDir>
+    <classFeature>ne-type</classFeature>
+    <layers>phenotypes,microorganism,habitats</layers>
+    <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
+  </html>
+
+  <words class="TabularExport">
+    <outDir>corpora/&corpus;/batch/&batch;</outDir>
+    <files>$</files>
+    <fileName>"words.txt"</fileName>
+    <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
+    <columns separator=";">
+      section.document.@id;
+      @form
+    </columns>
+  </words>
+
+  <bionlp-st-a2>
+    <habitats class="TabularExport">
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:habitats</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Habitat " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </habitats>
+    
+    <phenotypes class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:phenotypes</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Phenotype " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </phenotypes>
+    
+    <microorganisms class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:microorganism</lines>
+      <columns separator=";">
+	"T" ^ id:unique;
+	"Microorganism " ^ start ^ " " ^ end;
+	str:normalizeSpace(@form)
+      </columns>
+    </microorganisms>
+
+    <obt class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:habitats|layer:phenotypes</lines>
+      <columns separator=";">
+	"N" ^ id:unique;
+	"OntoBiotope Annotation:T" ^ id:unique ^ " Referent:" ^ @concept-id
+      </columns>
+    </obt>
+
+    <taxid class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>layer:microorganism</lines>
+      <columns separator=";">
+	"N" ^ id:unique;
+	"NCBI_Taxonomy Annotation:T" ^ id:unique ^ " Referent:" ^ str:replace(@taxid, "ncbi:", "")
+      </columns>
+    </taxid>
+
+    <lives-in class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>relations:CooccurrenceLocalization.tuples[args:Localization.@concept-id != ""]</lines>
+      <columns separator=";">
+	"R" ^ id:unique;
+	"Lives_In Microorganism:T" ^ args:Bacterium.id:unique ^ " Location:T" ^ args:Localization.id:unique
+      </columns>
+    </lives-in>
+
+    <exhibits class="TabularExport">
+      <append/>
+      <outDir>corpora/&corpus;/batch/&batch;/a2</outDir>
+      <files>documents.sections</files>
+      <fileName>document.@id ^ ".a2"</fileName>
+      <lines>relations:PhenotypeRelation.tuples</lines>
+      <columns separator=";">
+	"R" ^ id:unique;
+	"Exhibits Microorganism:T" ^ args:Microorganism.id:unique ^ " Property:T" ^ args:Phenotype.id:unique
+      </columns>
+    </exhibits>
+  </bionlp-st-a2>
 
 
   <success class="TabularExport">
diff --git a/process-evaluate_BioNLP-OST.snakefile b/process-evaluate_BioNLP-OST.snakefile
new file mode 100644
index 00000000..e9f494ff
--- /dev/null
+++ b/process-evaluate_BioNLP-OST.snakefile
@@ -0,0 +1,86 @@
+## local rule
+# localrules: all, concat_results
+
+## config file
+configfile: "config/config.yaml"
+
+## document batches
+BATCHES, = glob_wildcards(config["BIONLPOST_BATCHES_HOME"] + "/{id}/bionlp-st")
+
+
+'''
+all
+'''
+rule all:
+	input:
+		log=expand("corpora/BioNLP-OST-2019/batch/{B}/eval.json", B=BATCHES),
+                scores=expand("corpora/BioNLP-OST-2019/batch/{B}/eval.json", B=BATCHES)
+
+
+'''
+Extract entities in different corpus 
+batches using the alvisnlp plan (entities.plan)
+'''
+rule run_bionlp_prediction:
+	input:
+		dir=directory("corpora/BioNLP-OST-2019/batch/{B}/bionlp-st"),
+		xslt="corpora/microbes-2019/microbes-2019-pubmed2alvisnlp.xslt"
+	output:
+		relations="corpora/BioNLP-OST-2019/batch/{B}/relations.txt",
+		phenotypeRelations="corpora/BioNLP-OST-2019/batch/{B}/phenotype-relations.txt",
+		usesRelations="corpora/BioNLP-OST-2019/batch/{B}/uses-relations.txt",
+		microorganisms="corpora/BioNLP-OST-2019/batch/{B}/microorganisms.txt",
+		habitats="corpora/BioNLP-OST-2019/batch/{B}/habitats.txt",
+		phenotypes="corpora/BioNLP-OST-2019/batch/{B}/phenotypes.txt",
+		uses="corpora/BioNLP-OST-2019/batch/{B}/uses.txt",
+		index=directory("corpora/BioNLP-OST-2019/batch/{B}/index"),
+		a2=directory("corpora/BioNLP-OST-2019/batch/{B}/a2")
+	log:"corpora/BioNLP-OST-2019/batch/{B}/alvisnlp.log"
+	params:
+		batch="{B}",
+		corpus='BioNLP-OST-2019',
+                inhibitSyntax='inhibit-syntax',
+		onto='ancillaries/BioNLP-OST+EnovFood',
+                ontobiotopeUse='ancillaries/Use_V2',
+		plan='plans/entities.plan',
+		dir='corpora/BioNLP-OST-2019/batch/{B}/',
+		taxid_microorganisms='ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt',
+                taxa_id_full='ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt'
+	singularity:config["SINGULARITY_IMG"]
+	shell:"""
+		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
+		-log {log} \
+		-alias format bionlp-st \
+		-alias input-dir {input.dir} \
+		-alias input-xslt {input.xslt} \
+		-alias outputDir {params.dir} \
+		-environmentEntities \
+		-entity corpus {params.corpus} \
+		-feat inhibit-syntax {params.inhibitSyntax} \
+		-entity ontobiotope {params.onto} \
+		-entity ontobiotope-use {params.ontobiotopeUse} \
+		-entity batch {params.batch} \
+		-alias taxid_microorganisms {params.taxid_microorganisms} \
+		-alias taxa+id_full {params.taxa_id_full} \
+		{params.plan}	    
+	      """
+
+rule archive_prediction:
+    input:
+        a2=directory("corpora/BioNLP-OST-2019/batch/{B}/a2")
+    output:
+        zip="corpora/BioNLP-OST-2019/batch/{B}/predictions.zip"
+    shell:
+        """zip -9 {output.zip} {input.a2}/*.a2"""
+
+        
+rule evaluate:
+    input:
+        zip="corpora/BioNLP-OST-2019/batch/{B}/predictions.zip"
+    output:
+        scores="corpora/BioNLP-OST-2019/batch/{B}/eval.json"
+    params:
+        api=config["BIONLPOST_API"],
+        task="{B}"
+    shell:
+        """curl -o {output.scores} -X POST "{params.api}/task/{params.task}/test/evaluate" -H "accept: application/json" -H "Content-Type: multipart/form-data" -F "resamples=0" -F "detailed=false" -F "alternate=true" -F "zipfile=@{input.zip};type=application/zip" """
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 9ae857aa..9cda4f24 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -57,6 +57,7 @@ rule run_pubmed_entities:
 	shell:"""
 		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
 		-log {log} \
+		-alias format pubmed \
 		-alias input {input.file} \
 		-alias input-xslt {input.xslt} \
 		-alias outputDir {params.dir} \
-- 
GitLab


From c9b73cf9731eed2c68d72c89626d656f1125143b Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:08:50 +0100
Subject: [PATCH 32/64] documented BioNLP-OST evaluation

---
 README.md                    |  3 ++
 docs/7-process-bionlp-ost.md | 75 ++++++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 docs/7-process-bionlp-ost.md

diff --git a/README.md b/README.md
index 6c211ffd..a44c5812 100644
--- a/README.md
+++ b/README.md
@@ -31,6 +31,9 @@ We use [Snakemake](https://snakemake.readthedocs.io) pipelines to materialize th
 6. **`Process PubMed corpus`** to extract microorganisms, habitats of texts from Pubmed. 
 [details here...](docs/6-process-pubmed-data.md)
 
+7. **`Process BioNLP-OST 2019 test corpus`** to evaluate the results on a reference dataset. 
+[details here...](docs/7-process-bionlp-ost.md)
+
 
 The workflow relies on the following `structure of folders` to manage the resources:
 ```
diff --git a/docs/7-process-bionlp-ost.md b/docs/7-process-bionlp-ost.md
new file mode 100644
index 00000000..f2736d4a
--- /dev/null
+++ b/docs/7-process-bionlp-ost.md
@@ -0,0 +1,75 @@
+## About
+This pipeline is the same as the PubMed processing one, using the same alvisnlp plan `plans/entities.plan`.
+Rather than processing PubMed abstracts, it processes the test data from three tasks of the [BioNLP-OST 2019 Bacteria Biotope](https://sites.google.com/view/bb-2019/home), then evaluates the prediction with the API of the dedicated [online evaluation tool](http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/index.html).
+
+The three tasks are:
+* `BB-norm+ner`: evaluates NER and normalization (Microorganism, Habitat and Phenotype).
+* `BB-rel+ner`: evaluates NER and relation extraction (Lives_In and Exhibits).
+* `BB-kb+ner`: evaluates knowledge base extraction performance.
+
+The three datasets are available in `corpora/BioNLP-OST-2019/batch`. 
+
+## Run the pipeline
+
+```
+snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 30 --jobs 3 \
+--snakefile process-evaluate_BioNLP-OST.snakefile \
+--cluster "qsub -v PYTHONPATH=''  -V -cwd -e log/ -o log/ -q short.q -pe thread 2" \
+--restart-times 4 all
+```
+## Display the DAG
+
+```
+snakemake --verbose \
+--dag \
+--printshellcmds \
+--use-singularity \
+--forceall \
+--nolock \
+--dry-run \
+--reason \
+--cores 4  \
+--snakefile  process-evaluate_BioNLP-OST.snakefile \
+all
+| dot -Tsvg >  process-evaluate_BioNLP-OST.snakefile.svg
+
+show  process-evaluate_BioNLP-OST.snakefile.svg
+```
+
+## **Resources used**
+
+The pipeline relies on the following alvisnlp plan:
+* `entities.plan`
+	* `taxa.plan`
+		* `strains-1.plan`
+	* `syntax.plan`
+		* `segmentation.plan`
+			* `number-and-dates.plan`
+	* `strains-2.plan`
+	* `pos-tag-lemma-postprocessing.plan`
+	* `tomap-habitats.plan`
+		* `tag-food-derivative.plan`
+		* `tag-food-process.plan`
+	* `tomap-microbial-phenotypes.plan`
+	* `use-extraction.plan`
+	* `anaphora.plan`
+
+The pipeline handles the following resources :
+* inputs
+    * `corpora/BioNLP-OST-2019/*/bionlp-st`
+    * `ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+    * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo`
+    * `ancillaries/Use_V2.obo`
+* outputs
+	* `corpora/BioNLP-OST-2019/batch/*/eval.json`
+* programs
+    * `alvisnlp singularity container`
+    * `python env`
+
+
+|solution |nb steps |
+|--------|--------|
+|AlvisNLP plans | xxx |
+|bash scripts| xxx |
+|python scripts | xxx |
+| java jars | xxx |
-- 
GitLab


From 02addde30eaf12b36325bf83f592e4b3187a3dd3 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:17:09 +0100
Subject: [PATCH 33/64] ignore more output files

---
 .gitignore | 51 +++++++++++++++++++++++++++------------------------
 1 file changed, 27 insertions(+), 24 deletions(-)

diff --git a/.gitignore b/.gitignore
index 09e7e901..633dc797 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,30 +19,33 @@ corpora/genbank/mapped_habitats.txt
 corpora/genbank/mapped_taxids.txt
 corpora/genbank/taxids.txt
 corpora/genbank/test-3.2.txt
-corpora/microbes-2019/batch/*/adb/
-corpora/microbes-2019/batch/*/alvisnlp.log
-corpora/microbes-2019/batch/*/anaphora.txt
-corpora/microbes-2019/batch/*/bacteria.txt
-corpora/microbes-2019/batch/*/dependencies.txt
-corpora/microbes-2019/batch/*/doc-mesh.txt
-corpora/microbes-2019/batch/*/geo.txt
-corpora/microbes-2019/batch/*/habitats.txt
-corpora/microbes-2019/batch/*/index-food/
-corpora/microbes-2019/batch/*/index/
-corpora/microbes-2019/batch/*/microorganisms-short.txt
-corpora/microbes-2019/batch/*/microorganisms.txt
-corpora/microbes-2019/batch/*/phenotype-relations.txt
-corpora/microbes-2019/batch/*/phenotypes.txt
-corpora/microbes-2019/batch/*/relations.txt
-corpora/microbes-2019/batch/*/sentences.txt
-corpora/microbes-2019/batch/*/success.txt
-corpora/microbes-2019/batch/*/taxa.txt
-corpora/microbes-2019/batch/*/uses-relations.txt
-corpora/microbes-2019/batch/*/uses.txt
-corpora/microbes-2019/batch/*/words.txt
-corpora/microbes-2019/batch/*/yatea-var/
-corpora/microbes-2019/batch/*/yatea/
-corpora/microbes-2019/expander/
+corpora/*-2019/batch/*/adb/
+corpora/*-2019/batch/*/alvisnlp.log
+corpora/*-2019/batch/*/anaphora.txt
+corpora/*-2019/batch/*/bacteria.txt
+corpora/*-2019/batch/*/dependencies.txt
+corpora/*-2019/batch/*/doc-mesh.txt
+corpora/*-2019/batch/*/geo.txt
+corpora/*-2019/batch/*/habitats.txt
+corpora/*-2019/batch/*/index-food/
+corpora/*-2019/batch/*/index/
+corpora/*-2019/batch/*/microorganisms-short.txt
+corpora/*-2019/batch/*/microorganisms.txt
+corpora/*-2019/batch/*/phenotype-relations.txt
+corpora/*-2019/batch/*/phenotypes.txt
+corpora/*-2019/batch/*/relations.txt
+corpora/*-2019/batch/*/sentences.txt
+corpora/*-2019/batch/*/success.txt
+corpora/*-2019/batch/*/taxa.txt
+corpora/*-2019/batch/*/uses-relations.txt
+corpora/*-2019/batch/*/uses.txt
+corpora/*-2019/batch/*/words.txt
+corpora/*-2019/batch/*/yatea-var/
+corpora/*-2019/batch/*/yatea/
+corpora/*-2019/expander/
+corpora/*-2019/batch/*/a2/
+corpora/BioNLP-OST-2019/batch/*/eval.json
+corpora/BioNLP-OST-2019/batch/*/predictions.zip
 corpora/microbes-2019/*.full.txt
 corpora/microbes-2019/index/
 .snakemake/
-- 
GitLab


From 1742a6eae3113f0faed7374b5ea34f293d5fcb61 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 13:20:51 +0100
Subject: [PATCH 34/64] ignore some softwares

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 633dc797..e2b67045 100644
--- a/.gitignore
+++ b/.gitignore
@@ -64,3 +64,6 @@ ancillaries/yatea-ncbi/
 ancillaries/yatea-var/
 ancillaries/yatea/
 yatea-train/
+softwares/alvisir-install/
+softwares/*.sif
+softwares/obo-utils
-- 
GitLab


From 56c38dffe6e2ef53fd5d08476bd6a30089e296b6 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 13 Jan 2021 14:00:40 +0100
Subject: [PATCH 35/64] create dummy bionlp-st directory

---
 process_PubMed_corpus.snakefile | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 9cda4f24..b5a20ac3 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -23,7 +23,14 @@ rule all:
 		florilege_Habitat_result="corpora/florilege/pubmed/PubMed-Habitat.txt",
 		florilege_Phenotype_result="corpora/florilege/pubmed/PubMed-Phenotype.txt",
 		florilege_Use_result="corpora/florilege/pubmed/PubMed-Use.txt"
-		
+
+
+rule create_dummy_bionlp_st_dir:
+    output:
+        dummy=directory("corpora/microbes-2019/batch/{B}/bionlp-st")
+    shell:
+        '''mkdir -p {output.dummy}'''
+
 
 '''
 Extract entities in different corpus 
@@ -32,6 +39,7 @@ batches using the alvisnlp plan (entities.plan)
 rule run_pubmed_entities:
 	input:
 		file="corpora/microbes-2019/batch/{B}/batch.xml",
+		dummy=("corpora/microbes-2019/batch/{B}/bionlp-st"),
 		xslt="corpora/microbes-2019/microbes-2019-pubmed2alvisnlp.xslt"
 	output:
 		relations="corpora/microbes-2019/batch/{B}/relations.txt",
@@ -54,7 +62,8 @@ rule run_pubmed_entities:
 		taxid_microorganisms='ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt',
                 taxa_id_full='ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt'
 	singularity:config["SINGULARITY_IMG"]
-	shell:"""
+	shell:
+            """
 		alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
 		-log {log} \
 		-alias format pubmed \
-- 
GitLab


From 20fee3cb8e36adf5c4b11283757e5ead575b16c9 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:04:20 +0100
Subject: [PATCH 36/64] Add new file

---
 corpora%2Fflorilege/labels.stats | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 corpora%2Fflorilege/labels.stats

diff --git a/corpora%2Fflorilege/labels.stats b/corpora%2Fflorilege/labels.stats
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/corpora%2Fflorilege/labels.stats
@@ -0,0 +1 @@
+
-- 
GitLab


From bb5cde58d30f4ae45ead63e27e85da3d85e69af8 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:05:03 +0100
Subject: [PATCH 37/64] Update labels.stats

---
 {corpora%2Fflorilege => corpora/florilege}/labels.stats | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {corpora%2Fflorilege => corpora/florilege}/labels.stats (100%)

diff --git a/corpora%2Fflorilege/labels.stats b/corpora/florilege/labels.stats
similarity index 100%
rename from corpora%2Fflorilege/labels.stats
rename to corpora/florilege/labels.stats
-- 
GitLab


From 825ae2ae8ad59ee1bb88d25fc331f8009a07f312 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 14:44:50 +0100
Subject: [PATCH 38/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 8b137891..7bd7b0cb 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1 +1,24 @@
+id,label,file
+cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
+cirm_002,nombre d'entrées cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
+cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_taxids.txt
+cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
+cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
+cirm_006,nombre d'habitat de cirm-Levure,cirm/mapped_yeast_habitats.txt
+genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
+genbank_002,nombre de taxon de genbank,genbank/mapped_taxids.txt
+genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
+dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
+dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
+dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
+pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
+pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
+pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
+pubmed_004,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
+pubmed_005,nombre de relations du type #Phenotype-Relations pubmed,microbes-2019/phenotype-relations.txt
+pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
+pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
+pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
+pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
+
 
-- 
GitLab


From 3f5ee3d6b29805977ff4d90f684c656c00af5140 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 24 Feb 2021 15:42:33 +0100
Subject: [PATCH 39/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 7bd7b0cb..7ca2a12a 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -20,5 +20,14 @@ pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotyp
 pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
 pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
-
-
+eval_001, corpus utilisés, BioNLP-OST-2019
+eval_002, date, None
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-- 
GitLab


From 73991f60022df60a7ba2770d959f75b5ecbf0695 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 10:21:46 +0100
Subject: [PATCH 40/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 7ca2a12a..fe279abc 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -26,8 +26,8 @@ eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-201
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
 eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
 eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-norm+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-- 
GitLab


From bdd127f432891ecf4acc3425cc4185a1d23104f0 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:03:30 +0100
Subject: [PATCH 41/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 32 ++++++++++++++++++++++++++------
 1 file changed, 26 insertions(+), 6 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9ce6bc95..e107cfdb 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -11,16 +11,35 @@ rule all:
 SOURCES=["cirm", "genbank", "dsmz", "microbes-2019"]
 
 '''
-cirm | nb entrees | count_lines(corpora/cirm/2019-07-05/extraction_3-fv.csv)
-cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2017/data_CIRM_levures_extraction_09032017.csv)
+cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx)
+cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
+'''
+ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
+rule count_lines_cirm:
+	input:
+		file="corpora/cirm/{file}"
+	output:
+		stats="corpora/cirm/stats/{file}_stats.csv"
+	params:
+		result="cirm/{file}",
+		c0="source",
+		v0="cirm",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+'''
 cirm | nb entites | count_lines(corpora/cirm/mapped_taxids.txt)
-cirm | nb yeast entities | count_lines(corpora/cirm/yeast_taxa.txt)
+cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-ENTREES_CIRM = ["2019-07-05/extraction_3-fv.csv", "Levures_2017/data_CIRM_levures_extraction_09032017.csv"]
-SORTIES_CIRM = ["mapped_taxids.txt", "yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
-FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
+SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
 rule count_lines_cirm:
@@ -41,6 +60,7 @@ rule count_lines_cirm:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
 '''
 merge
 '''
-- 
GitLab


From 60a784b8a2f9cad8b991abb3201f87c44817e12a Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:06:33 +0100
Subject: [PATCH 42/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index e107cfdb..a3460936 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -76,11 +76,11 @@ rule merge_stats_cirm:
 		result.to_csv(output.result, index=False)
 
 '''
-genbank | nb entrees | count_lines(corpora/genbank/req1_sup800_bacteria-descriptors.csv)
+genbank | nb entrees | count_lines(corpora/genbank/corpora/genbank/GenBank_extraction_20210127.tsv)
 genbank | nb entites | count_lines(corpora/genbank/mapped_taxids.txt)
 genbank | nb habitats | count_lines(corpora/genbank/mapped_habitats.txt)
 '''
-ENTREES_GENBANK = ["req1_sup800_bacteria-descriptors.csv"]
+ENTREES_GENBANK = ["corpora/genbank/GenBank_extraction_20210127.tsv"]
 SORTIES_GENBANK = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_GENBANK = ENTREES_GENBANK + SORTIES_GENBANK
 '''
-- 
GitLab


From d2000f6a970d1d2933c9916267dc121329955805 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 11:31:03 +0100
Subject: [PATCH 43/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 63 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 58 insertions(+), 5 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index a3460936..b0bdda44 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -15,7 +15,7 @@ cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_
 cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
 '''
 ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
-rule count_lines_cirm:
+rule stats_cirm:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -42,7 +42,7 @@ cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
-rule count_lines_cirm:
+rule stats_cirm:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -85,7 +85,7 @@ SORTIES_GENBANK = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_GENBANK = ENTREES_GENBANK + SORTIES_GENBANK
 '''
 '''
-rule count_lines_genbank:
+rule stats_genbank:
 	input:
 		file="corpora/genbank/{file}"
 	output:
@@ -127,7 +127,7 @@ SORTIES_DSMZ = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_DSMZ = ENTREES_DSMZ + SORTIES_DSMZ
 '''
 '''
-rule count_lines_dsmz:
+rule stats_dsmz:
 	input:
 		file="corpora/dsmz/{file}"
 	output:
@@ -179,7 +179,7 @@ FILES_PUBMED = ENTREES_PUBMED + SORTIES_PUBMED
 '''
 '''
 
-rule count_lines_pubmed:
+rule stats_pubmed:
 	input:
 		file="corpora/microbes-2019/{file}"
 	output:
@@ -212,6 +212,59 @@ rule merge_stats_pubmed:
 		result.to_csv(output.result, index=False)
 
 
+
+'''
+eval_001, corpus utilisés, BioNLP-OST-2019
+eval_002, date, None
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+'''
+ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
+SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
+FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
+
+'''
+'''
+
+rule stats_veal:
+	input:
+		file="corpora/microbes-2019/{file}"
+	output:
+		stats="corpora/microbes-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+'''
+merge
+'''
+rule merge_stats_eval:
+	input:
+		files=expand("corpora/microbes-2019/stats/{file}_stats.csv", file=FILES_PUBMED)
+	output:
+		result="corpora/microbes-2019/stats/stats.full.csv"
+	run:
+		import pandas
+		frames = [ pandas.read_csv(f) for f in input.files ]
+		result = pandas.concat(frames)
+		result.to_csv(output.result, index=False)
+
 '''
 merge all
 '''
-- 
GitLab


From cd7f6b82b388f3686b46e58dc722a8b0d224d286 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 18:15:15 +0100
Subject: [PATCH 44/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 89 ++++++++++++++++++++++++++++++++++------
 1 file changed, 77 insertions(+), 12 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index b0bdda44..f8e06321 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,3 +1,16 @@
+def get_score_stats(file, entity):
+	import json
+	data = json.load(open(file))
+	for d in (data['evaluation'])['global-evaluations']:
+		for s in d['scorings']:
+			if s['name'] == entity:
+				list = s['measures']
+				list[0]
+
+
+
+
+
 '''
 all
 '''
@@ -216,15 +229,15 @@ rule merge_stats_pubmed:
 '''
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_001
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_002
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_003
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json#eval_BB19-norm+ner_004
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_001
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_002
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json#eval_BB19-rel+ner_003
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json#eval_BB19-kb+ner_001#eval_BB19-kb+ner_002
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json#eval_BB19-kb+ner_002
 '''
 ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
 SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
@@ -233,11 +246,62 @@ FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
 '''
 '''
 
-rule stats_veal:
+rule stats_eval_BB19-norm+ner:
 	input:
-		file="corpora/microbes-2019/{file}"
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
 	output:
-		stats="corpora/microbes-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_json(input.file)
+		df1["evaluation"]
+		for d in (data['evaluation'])['global-evaluations']:
+			for s in d['scorings']:
+				if s['name'] == "Habitats":
+					for e in s['measures']:
+						print(e['name'])
+						print(e['value'])
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+
+'''
+'''
+
+rule stats_eval_BB19-rel+ner:
+	input:
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json
+	output:
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+	params:
+		result="microbes-2019/{file}",
+		c0="source",
+		v0="pubmed",
+		c1="file",
+		c2="count",
+		c="line"
+	run:
+		import pandas
+		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
+		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		df2.to_csv(output.stats, index=False)
+
+
+'''
+'''
+
+rule stats_eval_BB19-kb+ner:
+	input:
+		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+	output:
+		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
 		c0="source",
@@ -251,6 +315,7 @@ rule stats_veal:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+
 '''
 merge
 '''
-- 
GitLab


From 7ce29979b067580d4d852e63fad40225a5eb4769 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 20:10:07 +0100
Subject: [PATCH 45/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index f8e06321..09581902 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,11 +1,12 @@
-def get_score_stats(file, entity):
+def get_score_stats(file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", entity="Habitats"):
 	import json
 	data = json.load(open(file))
 	for d in (data['evaluation'])['global-evaluations']:
-		for s in d['scorings']:
+		scorings = d['scorings']
+		for s in scorings:
 			if s['name'] == entity:
-				list = s['measures']
-				list[0]
+				return s['measures'][0]
+	return None
 
 
 
-- 
GitLab


From 1160b44ff315d2f637d349283cb3715d741e0b4b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 25 Feb 2021 20:22:57 +0100
Subject: [PATCH 46/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 09581902..5311c9ba 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -261,14 +261,9 @@ rule stats_eval_BB19-norm+ner:
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_json(input.file)
-		df1["evaluation"]
-		for d in (data['evaluation'])['global-evaluations']:
-			for s in d['scorings']:
-				if s['name'] == "Habitats":
-					for e in s['measures']:
-						print(e['name'])
-						print(e['value'])
+		get_score_stats(input.file, "Habitats")
+		get_score_stats(input.file, "Phenotypes")
+		get_score_stats(input.file, "Microorganisms")
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
-- 
GitLab


From 8b19087aa1812edc0cd1ce470231967a702e8275 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:06:30 +0100
Subject: [PATCH 47/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 77 +++++++++++++++++++---------------------
 1 file changed, 36 insertions(+), 41 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 5311c9ba..743c801b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,16 +1,3 @@
-def get_score_stats(file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", entity="Habitats"):
-	import json
-	data = json.load(open(file))
-	for d in (data['evaluation'])['global-evaluations']:
-		scorings = d['scorings']
-		for s in scorings:
-			if s['name'] == entity:
-				return s['measures'][0]
-	return None
-
-
-
-
 
 '''
 all
@@ -22,7 +9,7 @@ rule all:
 
 
 
-SOURCES=["cirm", "genbank", "dsmz", "microbes-2019"]
+SOURCES=["cirm", "genbank", "dsmz", "microbes-2019", "BioNLP-OST-2019"]
 
 '''
 cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx)
@@ -242,84 +229,92 @@ eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/ev
 '''
 ENTREES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner", "BioNLP-OST-2019/batch/BB19-rel+ner", "BioNLP-OST-2019/batch/BB19-kb+ner"]
 SORTIES_EVAL = ["BioNLP-OST-2019/batch/BB19-norm+ner/eval.json", "BioNLP-OST-2019/batch/BB19-rel+ner/eval.json", "BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"]
-FILES_EVAL = ENTREES_PUBMED + SORTIES_PUBMED
+FILES_EVAL = ["BB19-norm+ner", "BB19-rel+ner", "BB19-kb+ner"]
+
+def get_score_stats(file, entity):
+	import json
+	data = json.load(open(file))
+	for d in (data['evaluation'])['global-evaluations']:
+		scorings = d['scorings']
+		for s in scorings:
+			if s['name'] == entity:
+				return s['measures'][0]
+	return None
+
 
 '''
 '''
-
 rule stats_eval_BB19-norm+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-norm+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-norm+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		get_score_stats(input.file, "Habitats")
-		get_score_stats(input.file, "Phenotypes")
-		get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		h = get_score_stats(input.file, "Habitats")
+		p = get_score_stats(input.file, "Phenotypes")
+		m = get_score_stats(input.file, "Microorganisms")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
 '''
 '''
-
 rule stats_eval_BB19-rel+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json
+		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-rel+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-rel+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		l = get_score_stats(input.file, "Lives_In")
+		e = get_score_stats(input.file, "Exhibits")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
 '''
 '''
-
 rule stats_eval_BB19-kb+ner:
 	input:
-		file="corpora/BioNLP-OST-2019/batch/{file}/eval.json"
+		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-		stats="corpora/BioNLP-OST-2019/stats/{file}_stats.csv"
+		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
-		result="microbes-2019/{file}",
+		result="BioNLP-OST-2019/BB19-kb+ner",
 		c0="source",
-		v0="pubmed",
+		v0="BB19-kb+ner",
 		c1="file",
 		c2="count",
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
-		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
+		s = get_score_stats(input.file, "Standard scoring")
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring"], params.c2: [s['name'], s['value']]})
 		df2.to_csv(output.stats, index=False)
 
-
 '''
 merge
 '''
 rule merge_stats_eval:
 	input:
-		files=expand("corpora/microbes-2019/stats/{file}_stats.csv", file=FILES_PUBMED)
+		files=expand("corpora/BioNLP-OST-2019/stats/{file}_stats.csv", file=FILES_EVAL)
 	output:
-		result="corpora/microbes-2019/stats/stats.full.csv"
+		result="corpora/BioNLP-OST-2019/stats/stats.full.csv"
 	run:
 		import pandas
 		frames = [ pandas.read_csv(f) for f in input.files ]
-- 
GitLab


From 37f56d2705419b7402cf7ed643d71d841434a41e Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:35:50 +0100
Subject: [PATCH 48/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 743c801b..c82c0a44 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -243,6 +243,7 @@ def get_score_stats(file, entity):
 
 
 '''
+
 '''
 rule stats_eval_BB19-norm+ner:
 	input:
@@ -266,6 +267,7 @@ rule stats_eval_BB19-norm+ner:
 
 
 '''
+
 '''
 rule stats_eval_BB19-rel+ner:
 	input:
@@ -288,6 +290,7 @@ rule stats_eval_BB19-rel+ner:
 
 
 '''
+
 '''
 rule stats_eval_BB19-kb+ner:
 	input:
-- 
GitLab


From beca89a6a213f22bddeff5af2418c1ded45cfad3 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:41:50 +0100
Subject: [PATCH 49/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index c82c0a44..8dee3107 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -245,7 +245,7 @@ def get_score_stats(file, entity):
 '''
 
 '''
-rule stats_eval_BB19-norm+ner:
+rule stats_eval_BB19-norm:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
@@ -269,7 +269,7 @@ rule stats_eval_BB19-norm+ner:
 '''
 
 '''
-rule stats_eval_BB19-rel+ner:
+rule stats_eval_BB19-rel:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
@@ -292,7 +292,7 @@ rule stats_eval_BB19-rel+ner:
 '''
 
 '''
-rule stats_eval_BB19-kb+ner:
+rule stats_eval_BB19-kb:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-- 
GitLab


From 54f1f90c7c050ca389c0079690674f085c7cde04 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:43:28 +0100
Subject: [PATCH 50/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 8dee3107..d5ca3ef7 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -245,7 +245,7 @@ def get_score_stats(file, entity):
 '''
 
 '''
-rule stats_eval_BB19-norm:
+rule stats_eval_BB19_norm:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-norm+ner/eval.json"
 	output:
@@ -269,7 +269,7 @@ rule stats_eval_BB19-norm:
 '''
 
 '''
-rule stats_eval_BB19-rel:
+rule stats_eval_BB19_rel:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-rel+ner/eval.json"
 	output:
@@ -292,7 +292,7 @@ rule stats_eval_BB19-rel:
 '''
 
 '''
-rule stats_eval_BB19-kb:
+rule stats_eval_BB19_kb:
 	input:
 		file="corpora/BioNLP-OST-2019/batch/BB19-kb+ner/eval.json"
 	output:
-- 
GitLab


From 728d899f749abc8b764e888c2ce5f5d7aab8f200 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:44:33 +0100
Subject: [PATCH 51/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index d5ca3ef7..ed649192 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -16,7 +16,7 @@ cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_
 cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
 '''
 ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
-rule stats_cirm:
+rule stats_cirm_BIA:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -40,7 +40,7 @@ cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-SORTIES_CIRM = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
+SORTIES_CIRM_Levure = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
 rule stats_cirm:
-- 
GitLab


From 6f79b53ed528252dff4a3b463de0ec54fd0cd664 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 11:46:17 +0100
Subject: [PATCH 52/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index ed649192..9f2b51a7 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -40,10 +40,10 @@ cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
 cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
 cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
 '''
-SORTIES_CIRM_Levure = ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
+SORTIES_CIRM= ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
 '''
 '''
-rule stats_cirm:
+rule stats_cirm_Levure:
 	input:
 		file="corpora/cirm/{file}"
 	output:
@@ -61,6 +61,7 @@ rule stats_cirm:
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
+
 FILES_CIRM = ENTREES_CIRM + SORTIES_CIRM
 '''
 merge
-- 
GitLab


From 7d1e09c0dfc48cb4874d8418b48492f82d989463 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:34:23 +0100
Subject: [PATCH 53/64] Update corpora/florilege/labels.stats

---
 corpora/florilege/labels.stats | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index fe279abc..ab0e1c2f 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -22,12 +22,12 @@ pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner/eval.json
-eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner/eval.json
-eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
-eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner/eval.json
+eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
+eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
+eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
+eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
+eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
+eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
+eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
-- 
GitLab


From b2f8d1003c5c826ec60aa05565f3ec6282c8a1b7 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:50:20 +0100
Subject: [PATCH 54/64] Update generate_stats.snakefile,
 corpora/florilege/labels.stats files

---
 corpora/florilege/labels.stats | 2 ++
 generate_stats.snakefile       | 8 +++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index ab0e1c2f..022ffe6b 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -23,10 +23,12 @@ pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-rela
 eval_001, corpus utilisés, BioNLP-OST-2019
 eval_002, date, None
 eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
+eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
 eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
 eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
 eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
+eval_BB19-rel+ner_002, score global sur la prédiction de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Standard_scoring
 eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
 eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
 eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9f2b51a7..29d17b67 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -260,10 +260,11 @@ rule stats_eval_BB19_norm:
 		c="line"
 	run:
 		import pandas
+		s = get_score_stats(input.file, "Standard scoring")
 		h = get_score_stats(input.file, "Habitats")
 		p = get_score_stats(input.file, "Phenotypes")
 		m = get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], h['value'], p['value'], m['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -284,9 +285,10 @@ rule stats_eval_BB19_rel:
 		c="line"
 	run:
 		import pandas
+		s = get_score_stats(input.file, "Standard scoring")
 		l = get_score_stats(input.file, "Lives_In")
 		e = get_score_stats(input.file, "Exhibits")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], l['value'], e['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -347,7 +349,7 @@ merge
 rule joint_stats:
 	input:
 		full_r="corpora/florilege/stats.full.csv",
-		concepts="corpora/florilege/stats.labels"
+		concepts="corpora/florilege/labels.stats"
 	output:
 		result="corpora/florilege/full_stats_with_labels.csv"
 	run:
-- 
GitLab


From a3093d1fbbfa1b9e25cfd6ef0991d0260e6610e0 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 26 Feb 2021 13:53:30 +0100
Subject: [PATCH 55/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 29d17b67..f221f73b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -264,7 +264,7 @@ rule stats_eval_BB19_norm:
 		h = get_score_stats(input.file, "Habitats")
 		p = get_score_stats(input.file, "Phenotypes")
 		m = get_score_stats(input.file, "Microorganisms")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Habitat", params.result+"#Phenotype", params.result+"#Microorganism"], params.c2: [h['name'], s['value'], h['value'], p['value'], m['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
@@ -288,7 +288,7 @@ rule stats_eval_BB19_rel:
 		s = get_score_stats(input.file, "Standard scoring")
 		l = get_score_stats(input.file, "Lives_In")
 		e = get_score_stats(input.file, "Exhibits")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", , params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
-- 
GitLab


From 3b46301a3cbe841e7d1cf7754f98cf5eb5d08fe4 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:14:43 +0000
Subject: [PATCH 56/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 81 ++++++++++++++++++++--------------------
 1 file changed, 40 insertions(+), 41 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index f221f73b..9e49550b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,4 +1,3 @@
-
 '''
 all
 '''
@@ -23,11 +22,11 @@ rule stats_cirm_BIA:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="source",
-		v0="cirm",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="CIRM",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
@@ -50,11 +49,11 @@ rule stats_cirm_Levure:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="source",
-		v0="cirm",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="CIRM",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -94,11 +93,11 @@ rule stats_genbank:
 		stats="corpora/genbank/stats/{file}_stats.csv"
 	params:
 		result="genbank/{file}",
-		c0="source",
-		v0="genbank",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="GENBANK",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -136,11 +135,11 @@ rule stats_dsmz:
 		stats="corpora/dsmz/stats/{file}_stats.csv"
 	params:
 		result="dsmz/{file}",
-		c0="source",
-		v0="dsmz",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="DSMZ",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -188,11 +187,11 @@ rule stats_pubmed:
 		stats="corpora/microbes-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
-		c0="source",
-		v0="pubmed",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="PUBMED",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -253,11 +252,11 @@ rule stats_eval_BB19_norm:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-norm+ner",
-		c0="source",
-		v0="BB19-norm+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-NORM+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -278,11 +277,11 @@ rule stats_eval_BB19_rel:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-rel+ner",
-		c0="source",
-		v0="BB19-rel+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-REL+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -302,11 +301,11 @@ rule stats_eval_BB19_kb:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-kb+ner",
-		c0="source",
-		v0="BB19-kb+ner",
-		c1="file",
-		c2="count",
-		c="line"
+		c0="SOURCE",
+		v0="BB19-KB+NER",
+		c1="FILE",
+		c2="LIBELLE",
+		c="LINE"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
-- 
GitLab


From 70a6326d0c130c8608ce8151d0faf34e334736f8 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:33:20 +0000
Subject: [PATCH 57/64] Update corpora/florilege/stats.labels,
 corpora/florilege/labels.stats, generate_stats.snakefile files

---
 corpora/florilege/labels.stats | 11 ++++++++---
 corpora/florilege/stats.labels |  2 +-
 generate_stats.snakefile       | 32 ++++++++++++++++----------------
 3 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 022ffe6b..b3c55895 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1,16 +1,20 @@
-id,label,file
+id,libelle,uri
+cirm_000, date de mise à jour des données de cirm, /db/maj/genbank/date
 cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
 cirm_002,nombre d'entrées cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
 cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_taxids.txt
 cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
 cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
 cirm_006,nombre d'habitat de cirm-Levure,cirm/mapped_yeast_habitats.txt
+genbank_000, date de mise à jour des données de genbank,/db/maj/genbank/date
 genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
 genbank_002,nombre de taxon de genbank,genbank/mapped_taxids.txt
 genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
+dsmz_000, date de mise à jour des données de dsmz,/db/maj/dsmz/date
 dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
 dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
 dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
+pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
 pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
 pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
 pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
@@ -20,8 +24,8 @@ pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotyp
 pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
 pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
 pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
-eval_001, corpus utilisés, BioNLP-OST-2019
-eval_002, date, None
+eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
+eval_002, date d'évaluation, migale/evaluation/BB19/date
 eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
 eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
 eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
@@ -33,3 +37,4 @@ eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,Bio
 eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
 eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
 eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
+ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/pubmed/date
diff --git a/corpora/florilege/stats.labels b/corpora/florilege/stats.labels
index 7feb5ea9..3be2a540 100644
--- a/corpora/florilege/stats.labels
+++ b/corpora/florilege/stats.labels
@@ -1,4 +1,4 @@
-label,file
+LIBELLE,file
 entrées cirm,cirm/2019-07-05/extraction_3-fv.csv
 entrées cirm (levure),cirm/Levures_2017/data_CIRM_levures_extraction_09032017.csv
 taxid cirm,cirm/mapped_taxids.txt
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 9e49550b..89e36661 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -24,8 +24,8 @@ rule stats_cirm_BIA:
 		result="cirm/{file}",
 		c0="SOURCE",
 		v0="CIRM",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -51,8 +51,8 @@ rule stats_cirm_Levure:
 		result="cirm/{file}",
 		c0="SOURCE",
 		v0="CIRM",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -95,8 +95,8 @@ rule stats_genbank:
 		result="genbank/{file}",
 		c0="SOURCE",
 		v0="GENBANK",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -137,8 +137,8 @@ rule stats_dsmz:
 		result="dsmz/{file}",
 		c0="SOURCE",
 		v0="DSMZ",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -189,8 +189,8 @@ rule stats_pubmed:
 		result="microbes-2019/{file}",
 		c0="SOURCE",
 		v0="PUBMED",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -254,8 +254,8 @@ rule stats_eval_BB19_norm:
 		result="BioNLP-OST-2019/BB19-norm+ner",
 		c0="SOURCE",
 		v0="BB19-NORM+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -279,8 +279,8 @@ rule stats_eval_BB19_rel:
 		result="BioNLP-OST-2019/BB19-rel+ner",
 		c0="SOURCE",
 		v0="BB19-REL+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
@@ -303,8 +303,8 @@ rule stats_eval_BB19_kb:
 		result="BioNLP-OST-2019/BB19-kb+ner",
 		c0="SOURCE",
 		v0="BB19-KB+NER",
-		c1="FILE",
-		c2="LIBELLE",
+		c1="URI",
+		c2="VALEUR",
 		c="LINE"
 	run:
 		import pandas
-- 
GitLab


From 791be3dc2e508b98cc3d1e3f2655b0d6d9686c3b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 10:36:55 +0000
Subject: [PATCH 58/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 80 ++++++++++++++++++++--------------------
 1 file changed, 40 insertions(+), 40 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 89e36661..33fe8e9a 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -22,11 +22,11 @@ rule stats_cirm_BIA:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="SOURCE",
-		v0="CIRM",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="cirm",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
@@ -49,11 +49,11 @@ rule stats_cirm_Levure:
 		stats="corpora/cirm/stats/{file}_stats.csv"
 	params:
 		result="cirm/{file}",
-		c0="SOURCE",
-		v0="CIRM",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="cirm",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -93,11 +93,11 @@ rule stats_genbank:
 		stats="corpora/genbank/stats/{file}_stats.csv"
 	params:
 		result="genbank/{file}",
-		c0="SOURCE",
-		v0="GENBANK",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="genbank",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -135,11 +135,11 @@ rule stats_dsmz:
 		stats="corpora/dsmz/stats/{file}_stats.csv"
 	params:
 		result="dsmz/{file}",
-		c0="SOURCE",
-		v0="DSMZ",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="dsmz",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -187,11 +187,11 @@ rule stats_pubmed:
 		stats="corpora/microbes-2019/stats/{file}_stats.csv"
 	params:
 		result="microbes-2019/{file}",
-		c0="SOURCE",
-		v0="PUBMED",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="pubmed",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		df1 = pandas.read_csv(input.file, names = [params.c], header=None)
@@ -252,11 +252,11 @@ rule stats_eval_BB19_norm:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-norm+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-norm+ner",
-		c0="SOURCE",
-		v0="BB19-NORM+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-norm+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -277,11 +277,11 @@ rule stats_eval_BB19_rel:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-rel+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-rel+ner",
-		c0="SOURCE",
-		v0="BB19-REL+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-rel+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
@@ -301,11 +301,11 @@ rule stats_eval_BB19_kb:
 		stats="corpora/BioNLP-OST-2019/stats/BB19-kb+ner_stats.csv"
 	params:
 		result="BioNLP-OST-2019/BB19-kb+ner",
-		c0="SOURCE",
-		v0="BB19-KB+NER",
-		c1="URI",
-		c2="VALEUR",
-		c="LINE"
+		c0="source",
+		v0="bb19-kb+ner",
+		c1="uri",
+		c2="valeur",
+		c="line"
 	run:
 		import pandas
 		s = get_score_stats(input.file, "Standard scoring")
-- 
GitLab


From c0c787fcf57c5a3626699dcfa5374f83e243f6b2 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 12:02:34 +0000
Subject: [PATCH 59/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 33fe8e9a..0f3be205 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -355,5 +355,5 @@ rule joint_stats:
 		import pandas
 		df1=pandas.read_csv(input.concepts)
 		df2=pandas.read_csv(input.full_r)
-		df = pandas.merge(df1, df2)
+		df = pandas.merge(df1, df2, on="uri", how="left")
 		df.to_csv(output.result, index=False)
-- 
GitLab


From e68cdf202c3271bfce1fa853a2b23f025f9a590f Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mouhamadou.ba@inra.fr>
Date: Thu, 4 Mar 2021 13:19:16 +0100
Subject: [PATCH 60/64] update ontobiotope

---
 ancillaries/BioNLP-OST+EnovFood-Habitat.obo   | 3674 +++++++++++++++-
 ancillaries/BioNLP-OST+EnovFood-Phenotype.obo |   16 +-
 .../BioNLP-OST+EnovFood-no-obsolete.obo       | 3687 ++++++++++++++++-
 3 files changed, 7269 insertions(+), 108 deletions(-)

diff --git a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo b/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
index 279bda6a..5ac41ce6 100644
--- a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000001
@@ -224,6 +223,7 @@ is_a: OBT:000006 ! artificial environment
 [Term]
 id: OBT:000067
 name: cultivated habitat
+synonym: "cultivated area" EXACT []
 is_a: OBT:000004 ! animal husbandry and agricultural habitat
 
 [Term]
@@ -722,7 +722,7 @@ is_a: OBT:000156 ! subterrestrial habitat
 [Term]
 id: OBT:000226
 name: ceiling tile
-is_a: OBT:000098 ! household good
+is_a: OBT:003617 ! environmental surface
 
 [Term]
 id: OBT:000227
@@ -1322,7 +1322,7 @@ is_a: OBT:000094 ! food for human
 
 [Term]
 id: OBT:000398
-name: prothesis
+name: prosthesis
 is_a: OBT:000108 ! medical equipment
 
 [Term]
@@ -1354,6 +1354,7 @@ is_a: OBT:000093 ! fish pond
 id: OBT:000407
 name: respiratory tract
 synonym: "respiratory" RELATED [TyDI:55563]
+synonym: "respiratory airway" RELATED []
 synonym: "respiratory tree" RELATED [TyDI:55564]
 is_a: OBT:000039 ! animal part
 
@@ -1476,6 +1477,7 @@ is_a: OBT:000110 ! medical sample
 id: OBT:000432
 name: starter culture
 synonym: "dry starter" RELATED [TyDI:52942]
+synonym: "starter" EXACT []
 is_a: OBT:000113 ! microflora
 
 [Term]
@@ -1698,6 +1700,7 @@ is_a: OBT:000190 ! anaerobic bioreactor
 [Term]
 id: OBT:000488
 name: anaerobic sludge blanket reactor
+synonym: "UASB reactor" EXACT []
 is_a: OBT:000190 ! anaerobic bioreactor
 
 [Term]
@@ -1748,7 +1751,7 @@ is_a: OBT:000332 ! lesion
 [Term]
 id: OBT:000498
 name: auricular prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000500
@@ -1773,6 +1776,7 @@ is_a: OBT:000208 ! bathroom equipment
 [Term]
 id: OBT:000504
 name: bathtub
+synonym: "bath tub" EXACT []
 is_a: OBT:000208 ! bathroom equipment
 
 [Term]
@@ -1888,7 +1892,7 @@ is_a: OBT:000340 ! meat and bone meal
 [Term]
 id: OBT:000528
 name: bone-anchored prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000529
@@ -2064,7 +2068,7 @@ is_a: OBT:000338 ! marine environment
 id: OBT:000564
 name: cochlear prosthesis
 synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003645 ! ocular prosthesis
 
 [Term]
 id: OBT:000565
@@ -2100,7 +2104,7 @@ is_a: OBT:000240 ! commodity and primary derivative thereof
 [Term]
 id: OBT:000571
 name: compost
-is_a: OBT:000365 ! organic matter
+is_a: OBT:000585 ! dead matter
 
 [Term]
 id: OBT:000572
@@ -2151,6 +2155,7 @@ is_a: OBT:000194 ! animal farm
 [Term]
 id: OBT:000584
 name: dairy starter culture
+synonym: "dairy starter" EXACT []
 is_a: OBT:000432 ! starter culture
 
 [Term]
@@ -2188,8 +2193,8 @@ is_a: OBT:000313 ! host associated biofilm
 
 [Term]
 id: OBT:000591
-name: dental prothesis
-is_a: OBT:000398 ! prothesis
+name: dental prosthesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000592
@@ -2661,7 +2666,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000701
 name: laryngeal prosthetic device
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000702
@@ -2758,11 +2763,13 @@ is_a: OBT:000364 ! organ
 [Term]
 id: OBT:000720
 name: maize feed
+synonym: "corn feed" NARROW []
 is_a: OBT:000229 ! cereal feed
 
 [Term]
 id: OBT:000721
 name: maize storage
+synonym: "corn storage" NARROW []
 is_a: OBT:000423 ! silo
 
 [Term]
@@ -2807,7 +2814,7 @@ is_a: OBT:000341 ! medical outfit
 
 [Term]
 id: OBT:000730
-name: membrane
+name: animal membrane
 is_a: OBT:000196 ! animal tissue
 
 [Term]
@@ -3003,7 +3010,7 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000786
 name: pacemaker
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003632 ! prosthetic cardiac device
 
 [Term]
 id: OBT:000787
@@ -3180,7 +3187,8 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000830
 name: prosthetic joint
-is_a: OBT:000398 ! prothesis
+synonym: "joint prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000831
@@ -3725,7 +3733,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000947
 name: veterinary drug
-is_a: OBT:000261 ! drug
+is_a: OBT:003680 ! veterinary product
 
 [Term]
 id: OBT:000948
@@ -4929,6 +4937,7 @@ is_a: OBT:000684 ! industrial equipment
 [Term]
 id: OBT:001190
 name: maize silage
+synonym: "corn silage" NARROW []
 is_a: OBT:000871 ! silage
 
 [Term]
@@ -4988,7 +4997,7 @@ is_a: OBT:000816 ! plant tissue
 [Term]
 id: OBT:001202
 name: mesentery
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001206
@@ -5058,7 +5067,7 @@ is_a: OBT:000710 ! lining
 id: OBT:001219
 name: mucous membrane
 synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001220
@@ -5229,7 +5238,7 @@ is_a: OBT:000642 ! gastrointestinal tract part
 [Term]
 id: OBT:001253
 name: peritoneum
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001254
@@ -5747,6 +5756,7 @@ is_a: OBT:000529 ! broncho-pulmonary segment
 id: OBT:001359
 name: treated wood
 is_a: OBT:000586 ! dead wood
+is_a: OBT:003742 ! wood waste
 
 [Term]
 id: OBT:001360
@@ -5877,7 +5887,7 @@ is_a: OBT:000694 ! invertebrate species
 [Term]
 id: OBT:001387
 name: yolk sac
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001388
@@ -6165,6 +6175,7 @@ is_a: OBT:001038 ! clean room
 [Term]
 id: OBT:001445
 name: birch
+synonym: "birch tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -6673,11 +6684,6 @@ id: OBT:001544
 name: eosinophil
 is_a: OBT:001134 ! granulocyte
 
-[Term]
-id: OBT:001545
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-
 [Term]
 id: OBT:001546
 name: fermented food
@@ -6746,6 +6752,7 @@ is_a: OBT:001097 ! factory
 [Term]
 id: OBT:001558
 name: food processing waste
+synonym: "food residue" RELATED []
 is_a: OBT:001157 ! industrial organic waste
 
 [Term]
@@ -6793,7 +6800,8 @@ is_a: OBT:001114 ! food rind
 [Term]
 id: OBT:001567
 name: fruit tree
-is_a: OBT:001360 ! tree
+comment: horticole meaning
+is_a: OBT:002699 ! cultivated plant
 
 [Term]
 id: OBT:001568
@@ -7300,6 +7308,7 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 [Term]
 id: OBT:001666
 name: oak
+synonym: "oak tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -7548,7 +7557,7 @@ is_a: OBT:001257 ! plankton
 [Term]
 id: OBT:001715
 name: pine forest
-is_a: OBT:001119 ! forest
+is_a: OBT:003881 ! conifer forest
 
 [Term]
 id: OBT:001716
@@ -7562,8 +7571,9 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 
 [Term]
 id: OBT:001718
-name: plant residue
-is_a: OBT:001258 ! plant material
+name: agricultural plant residue
+synonym: "agricultural plant waste" NARROW []
+is_a: OBT:000478 ! agricultural waste
 
 [Term]
 id: OBT:001719
@@ -7592,7 +7602,7 @@ is_a: OBT:001132 ! grain and primary derivative thereof
 
 [Term]
 id: OBT:001724
-name: potato
+name: potato plant
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -8007,8 +8017,8 @@ is_a: OBT:001045 ! confectionery
 
 [Term]
 id: OBT:001803
-name: sugar-beet
-synonym: "betroot" EXACT [TyDI:49625]
+name: sugar-beet plant
+synonym: "betroot plant" EXACT [TyDI:49625]
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -8085,7 +8095,8 @@ is_a: OBT:001159 ! industrial sludge
 
 [Term]
 id: OBT:001818
-name: textile industry
+name: textile mill
+synonym: "textile factory" NARROW []
 is_a: OBT:001097 ! factory
 
 [Term]
@@ -8943,8 +8954,9 @@ is_a: OBT:001621 ! livestock barn
 
 [Term]
 id: OBT:001988
-name: dairy industry
-synonym: "milk industry" RELATED [TyDI:55159]
+name: dairy processing plant
+synonym: "dairy factory" EXACT []
+synonym: "milk processing factory" RELATED [TyDI:55159]
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9170,7 +9182,7 @@ is_a: OBT:001446 ! bird
 
 [Term]
 id: OBT:002039
-name: food fermentation industry
+name: food fermentation factory
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9350,7 +9362,7 @@ is_a: OBT:001821 ! tick
 [Term]
 id: OBT:002073
 name: hay
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002074
@@ -9418,7 +9430,7 @@ is_a: OBT:001557 ! food processing factory
 id: OBT:002086
 name: industrial bakery
 synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:003759 ! bakery
 
 [Term]
 id: OBT:002087
@@ -9635,7 +9647,7 @@ is_a: OBT:001802 ! sugar confectionery
 
 [Term]
 id: OBT:002129
-name: meat industry
+name: meat processing plant
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -9940,7 +9952,7 @@ is_a: OBT:001717 ! pistachio and primary derivative thereof
 [Term]
 id: OBT:002190
 name: plant cutting
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002191
@@ -10102,7 +10114,7 @@ is_a: OBT:001744 ! rice based dish
 [Term]
 id: OBT:002225
 name: rice-plant residue
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002226
@@ -10237,7 +10249,7 @@ id: OBT:002251
 name: slaughter plant
 synonym: "abattoir" RELATED [TyDI:50262]
 synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:002129 ! meat processing plant
 
 [Term]
 id: OBT:002252
@@ -10344,7 +10356,7 @@ is_a: OBT:001556 ! food fermentation equipment
 [Term]
 id: OBT:002271
 name: straw
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002272
@@ -10829,7 +10841,7 @@ is_a: OBT:002018 ! environmental water with chemical property
 [Term]
 id: OBT:002372
 name: brewery
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:002373
@@ -11039,7 +11051,7 @@ is_a: OBT:002174 ! pastry product
 [Term]
 id: OBT:002414
 name: creamery
-is_a: OBT:001988 ! dairy industry
+is_a: OBT:001988 ! dairy processing plant
 
 [Term]
 id: OBT:002415
@@ -11506,6 +11518,7 @@ is_a: OBT:002126 ! marine fish meat
 [Term]
 id: OBT:002513
 name: maize
+synonym: "corn" NARROW []
 is_a: OBT:002120 ! maize and primary derivative thereof
 
 [Term]
@@ -12747,7 +12760,7 @@ name: endothelium
 synonym: "endothelial" RELATED [TyDI:52445]
 synonym: "vascular endothelium" EXACT [TyDI:52444]
 is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:002791
@@ -13150,6 +13163,7 @@ is_a: OBT:000710 ! lining
 [Term]
 id: OBT:002914
 name: maize plant
+synonym: "corn plant" NARROW []
 is_a: OBT:002771 ! cereal crop
 
 [Term]
@@ -13490,6 +13504,7 @@ name: hotspring
 synonym: "hot spring" EXACT [TyDI:49581]
 is_a: OBT:000625 ! extreme high temperature environment
 is_a: OBT:001333 ! spring
+is_a: OBT:002019 ! environmental water with physical property
 
 [Term]
 id: OBT:002992
@@ -14078,7 +14093,7 @@ is_a: OBT:001632 ! market garden plant
 
 [Term]
 id: OBT:003098
-name: gum margin
+name: gingival margin
 is_a: OBT:003055 ! gum tissue
 
 [Term]
@@ -14764,7 +14779,7 @@ id: OBT:003221
 name: peritrophic membrane
 is_a: OBT:000200 ! arthropod part
 is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:003222
@@ -14941,8 +14956,8 @@ is_a: OBT:002055 ! fungi as food
 [Term]
 id: OBT:003251
 name: cheese factory
-is_a: OBT:001988 ! dairy industry
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:001988 ! dairy processing plant
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:003252
@@ -15028,6 +15043,7 @@ is_a: OBT:003203 ! heavy metal contaminated soil
 id: OBT:003266
 name: mine waste water
 synonym: "mine wastewater" EXACT [TyDI:51583]
+synonym: "mine water" EXACT []
 is_a: OBT:001212 ! mine waste
 is_a: OBT:002754 ! waste water
 
@@ -16195,7 +16211,7 @@ is_a: OBT:003458 ! semi soft cheese
 
 [Term]
 id: OBT:003475
-name: Granular
+name: Granular cheese
 is_a: OBT:003450 ! hard cheese
 
 [Term]
@@ -16902,3 +16918,3561 @@ name: tejuino
 synonym: "tejuíno" EXACT [TyDI:51685]
 is_a: OBT:003410 ! corn beverage
 is_a: OBT:003596 ! fermented juice
+
+[Term]
+id: OBT:003602
+name: airway epithelium
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003603
+name: chicken breast meat
+is_a: OBT:002394 ! chicken meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003604
+name: turkey breast meat
+is_a: OBT:002631 ! turkey meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003605
+name: rice bran
+is_a: OBT:001458 ! bran
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003606
+name: lacrimal sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003607
+name: conjunctival sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003608
+name: aneurysmal sac
+synonym: "aneurysm sac" EXACT []
+synonym: "aortic sac" EXACT []
+is_a: OBT:000231 ! circulatory system part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003609
+name: abdominal air sac
+synonym: "air sac" EXACT []
+synonym: "thoracic air sac" EXACT []
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003610
+name: hernial sac
+is_a: OBT:000039 ! animal part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003611
+name: umbilical cord
+is_a: OBT:000463 ! urogenital tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003612
+name: umbilical cord blood
+is_a: OBT:000521 ! blood
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003613
+name: vocal cord
+is_a: OBT:000529 ! broncho-pulmonary segment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003615
+name: box lunch
+is_a: OBT:000788 ! packed lunch
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003617
+name: environmental surface
+is_a: OBT:000006 ! artificial environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003618
+name: ceramic tile
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003619
+name: ceramic wall tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003620
+name: ceramic roofing tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003621
+name: stainless steel surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003622
+name: PCV surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003623
+name: plasticized PVC
+synonym: "PVC plastic" NARROW []
+is_a: OBT:003622 ! PCV surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003624
+name: PVC film
+is_a: OBT:000787 ! packaging
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003625
+name: sealed concrete
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003626
+name: bamboo cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003627
+name: wood Cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003628
+name: plastic cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003629
+name: voice prosthesis
+is_a: OBT:003630 ! tracheoesophageal prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003630
+name: tracheoesophageal prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003631
+name: silicone rubber voice prosthesis
+is_a: OBT:003629 ! voice prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003632
+name: prosthetic cardiac device
+synonym: "intracardiac prosthesis" NARROW []
+synonym: "prosthetic cardiovascular device" NARROW []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003633
+name: prosthetic heart valve
+synonym: "heart valve prosthesis" NARROW []
+synonym: "prosthetic valve" NARROW []
+synonym: "valvular prosthesis" NARROW []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003634
+name: mitral valve prosthesis
+synonym: "mitral prosthesis" EXACT []
+is_a: OBT:003633 ! prosthetic heart valve
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003635
+name: aortic prosthetic valve
+synonym: "aortic valve prosthesis" EXACT []
+synonym: "arterial prosthesis" EXACT []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003636
+name: orthopedic prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003637
+name: othopedic implant
+is_a: OBT:003636 ! orthopedic prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003638
+name: hip prosthesis
+synonym: "prosthetic hip joint" EXACT []
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003639
+name: femoral prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003640
+name: knee prosthesis
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003641
+name: shoulder prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003642
+name: cranial prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003643
+name: penile prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003644
+name: testicular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003645
+name: ocular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003646
+name: prosthetic eye
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003647
+name: iris prosthesis
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003648
+name: orbital implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003649
+name: cochlear implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003650
+name: dental implant
+is_a: OBT:000591 ! dental prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003651
+name: palatal obturator prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003652
+name: breast prosthesis
+synonym: "mammary prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003653
+name: breast implant
+is_a: OBT:003652 ! breast prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003654
+name: suction-socket prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003655
+name: granular sludge
+is_a: OBT:001523 ! digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003656
+name: aerobic granular sludge
+is_a: OBT:001861 ! anaerobic digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003657
+name: aerobic granular sludge reactor
+synonym: "AGS reactor" EXACT []
+is_a: OBT:000180 ! aerobic bioreactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003658
+name: granular sludge bed reactor
+synonym: "EGSB reactor" EXACT []
+is_a: OBT:000488 ! anaerobic sludge blanket reactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003659
+name: public swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003660
+name: indoor swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003661
+name: shower bath
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003662
+name: public bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003663
+name: traditional public bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003664
+name: bath basin
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003665
+name: thermal bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003666
+name: thermal saline bath
+is_a: OBT:002592 ! saline water
+is_a: OBT:003665 ! thermal bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003667
+name: mineral bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003668
+name: spa bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003669
+name: seawater bath
+is_a: OBT:003105 ! marine water
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003670
+name: freshwater bath
+is_a: OBT:002455 ! freshwater
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003671
+name: open air bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003672
+name: spring bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003673
+name: hot water bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003674
+name: hot spring bath
+is_a: OBT:002990 ! hotspring
+is_a: OBT:003673 ! hot water bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003675
+name: hot spring spa bath
+is_a: OBT:003674 ! hot spring bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003676
+name: bath sponge
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003677
+name: bath tub heating
+is_a: OBT:000671 ! home heating system
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003678
+name: antiseptic bath
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003679
+name: chlorhexidine bath
+is_a: OBT:003678 ! antiseptic bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003680
+name: veterinary product
+is_a: OBT:000011 ! medical environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003681
+name: insecticide bath
+is_a: OBT:003680 ! veterinary product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003682
+name: antiseptic shower
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003683
+name: dyeing bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003684
+name: skin tannery bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003685
+name: bleach bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003689
+name: mango tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003690
+name: lemon tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003691
+name: peach tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003692
+name: apricot tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003693
+name: quince tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003694
+name: cherry tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003695
+name: khaki tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003696
+name: lime tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003697
+name: carrot plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003698
+name: broccoli plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003699
+name: brussel sprout plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003700
+name: chinese cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003701
+name: collard green plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003702
+name: head cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003703
+name: shallot plant
+is_a: OBT:001389 ! Allium
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003704
+name: fruiting vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003705
+name: courgette plant
+synonym: "zucchini plant" EXACT []
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003706
+name: cucumber plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003707
+name: gherkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003708
+name: melon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003709
+name: pumpkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003710
+name: sweet pepper plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003711
+name: watermelon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003712
+name: leafy vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003713
+name: celery plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003714
+name: spinach plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003715
+name: table water
+is_a: OBT:001530 ! drinking water
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003716
+name: garment factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003717
+name: dyeing factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003718
+name: traditional Chinese fermented cabbage
+is_a: OBT:002321 ! Chinese cabbage
+is_a: OBT:003096 ! fermented vegetable product
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003719
+name: nasal swab
+is_a: OBT:001228 ! nasal secretion
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003720
+name: rum factory
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003721
+name: whisky distillery
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003722
+name: liquor
+is_a: OBT:001397 ! alcoholic drink
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003723
+name: udder
+is_a: OBT:000723 ! mammalian part
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003724
+name: lactic starter
+is_a: OBT:000584 ! dairy starter culture
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003726
+name: plant residue from food processing
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003727
+name: grape pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003728
+name: apple pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003729
+name: olive pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003730
+name: grape must
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003731
+name: sugarcane bagasse
+synonym: "sugar cane bagasse" EXACT []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003732
+name: agave bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003733
+name: citrus bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003734
+name: soy bran
+is_a: OBT:000038 ! animal feed
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003735
+name: palm kernel press cake
+synonym: "residue from palm oil extraction" NARROW []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003736
+name: sugar beet pressed pulp
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003737
+name: cranberry press cake
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003738
+name: forage residue
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003739
+name: cotton plant waste
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003740
+name: cottonseed hull
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003741
+name: olive press cake
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003742
+name: wood waste
+is_a: OBT:000467 ! waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003743
+name: sawdust
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003744
+name: waste house wood
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003745
+name: construction wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003746
+name: demolition wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003747
+name: hazardous industrial waste
+is_a: OBT:000685 ! industrial waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003748
+name: agricultural woody waste
+is_a: OBT:000478 ! agricultural waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003749
+name: wood waste fiber
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003750
+name: transport structure
+is_a: OBT:000162 ! transport equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003751
+name: pallet
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003752
+name: shipping container
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003753
+name: wooden pallet
+is_a: OBT:003751 ! pallet
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003756
+name: wood barrel
+is_a: OBT:000434 ! storage equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003757
+name: oak barrel
+is_a: OBT:003756 ! wood barrel
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003759
+name: bakery
+is_a: OBT:001557 ! food processing factory
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003760
+name: traditional bakery
+is_a: OBT:003759 ! bakery
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003761
+name: traditional dairy
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003762
+name: dairy farm
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003763
+name: snowpack
+is_a: OBT:000881 ! snow
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003764
+name: conifer needle
+is_a: OBT:000807 ! phylloplane part
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003765
+name: agricultural fence
+is_a: OBT:001183 ! livestock habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003766
+name: ungulate
+is_a: OBT:002078 ! herbivore
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003767
+name: biome type forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003768
+name: alpine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003769
+name: tropical rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003770
+name: arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003771
+name: boreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003772
+name: coastal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003773
+name: cooler rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003774
+name: dune forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003775
+name: equatorial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003776
+name: montane forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003777
+name: hemiboreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003778
+name: high altitude forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003779
+name: humid lakeland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003780
+name: low mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003781
+name: subtropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003782
+name: taiga forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003783
+name: lowland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003784
+name: marshy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003785
+name: mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003786
+name: neotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003787
+name: paleotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003788
+name: savannah - forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003789
+name: subalpine forest
+synonym: "sub-alpine forest" EXACT []
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003790
+name: sub-Antarctic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003791
+name: warm sub-tropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003792
+name: dry forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003793
+name: semi - arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003794
+name: semiarid temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003795
+name: hill forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003796
+name: hot forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003797
+name: humid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003798
+name: inland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003799
+name: moist forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003800
+name: plain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003801
+name: pluvial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003802
+name: riverbank forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003803
+name: riverine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003804
+name: submerged forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003805
+name: temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003806
+name: underwater forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003807
+name: upland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003808
+name: volcanic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003809
+name: warm - temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003810
+name: wet forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003811
+name: wildland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003812
+name: drained forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003813
+name: soddy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003814
+name: natural and managed forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003815
+name: natural forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003816
+name: virgin forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003817
+name: uncontrolled forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003818
+name: undisturbed forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003819
+name: unmanaged forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003820
+name: unpolluted forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003821
+name: preserved forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003822
+name: protected forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003823
+name: native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003824
+name: intact forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003825
+name: primary forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003826
+name: primeval forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003827
+name: pristine area of native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003828
+name: pristine forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003829
+name: non-burnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003830
+name: unburnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003831
+name: managed forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003832
+name: man - made forest system
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003833
+name: municipal forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003834
+name: park forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003836
+name: periurban forest
+synonym: "peri-urban" EXACT []
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003837
+name: plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003838
+name: recreational forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003839
+name: reserve forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003840
+name: rural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003841
+name: semi-natural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003842
+name: suburban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003843
+name: urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003844
+name: village-adjacent forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003845
+name: village forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003846
+name: wood forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003847
+name: second-growth forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003848
+name: secondary forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003849
+name: early successional forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003850
+name: burnt forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003851
+name: artificial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003852
+name: commercial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003853
+name: commercial plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003854
+name: community forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003855
+name: disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003856
+name: disturbed urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003857
+name: historical forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003858
+name: human disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003859
+name: old forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003860
+name: mature forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003861
+name: mature forest of high conservation value
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003862
+name: mature old-growth forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003863
+name: young forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003864
+name: forest of given species
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003865
+name: alder forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003866
+name: angiosperm-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003867
+name: arboreal forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003868
+name: argan forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003869
+name: aspen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003870
+name: beach forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003871
+name: beech forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003872
+name: beech-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003873
+name: birch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003874
+name: boreonemoral forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003875
+name: bosque forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003876
+name: broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003877
+name: broadleaf forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003878
+name: Cercocarpus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003879
+name: chestnut forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003880
+name: cloud forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003881
+name: conifer forest
+synonym: "coniferous forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003883
+name: coppice forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003884
+name: cypress forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003885
+name: deciduous forest
+synonym: "deciduous specie forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003886
+name: deciduous dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003888
+name: herb-rich coniferous forest
+is_a: OBT:003881 ! conifer forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003890
+name: dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003892
+name: evergreen broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003893
+name: forest with dominant vegetation
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003894
+name: hardwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003896
+name: holm-oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003897
+name: kelp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003898
+name: larch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003899
+name: lucidophyllous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003900
+name: mangrove forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003901
+name: maple forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003902
+name: maso bamboo forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003903
+name: hemlock fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003904
+name: amabilis fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003906
+name: monodominant forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003907
+name: monospecific forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003908
+name: spruce forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003909
+name: Nothofagaceae forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003910
+name: Nothofagus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003911
+name: oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003912
+name: oak-hickory forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003914
+name: ombrophilous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003916
+name: papyrifera forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003917
+name: perennial forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003918
+name: riparian forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003919
+name: pure forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003920
+name: red pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003921
+name: redwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003922
+name: riparian woodland
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003923
+name: poplar forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003924
+name: sclerophyll forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003925
+name: seasonal dry tropical forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003926
+name: scrub forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003927
+name: semi-evergreen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003928
+name: semideciduous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003929
+name: stone pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003931
+name: tanoak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003932
+name: xeric forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003933
+name: xerophytic forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003934
+name: mix forest
+synonym: "mixed forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003935
+name: papilionoid legume tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003936
+name: leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003937
+name: tulip tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003938
+name: tea-oil tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003939
+name: tea plant
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003940
+name: Syzygiumcordatum tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003941
+name: shea butter tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003942
+name: rubber tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003943
+name: riparian tree specie
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003944
+name: Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003945
+name: Prosopis tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003946
+name: peepal tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003947
+name: Pandanus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003948
+name: pacara earpod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003949
+name: Olea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003950
+name: Nothofagus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003951
+name: mopane tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003952
+name: Masson pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003953
+name: manuka tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003954
+name: loquat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003955
+name: lodgepole pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003956
+name: lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003957
+name: Katsura tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003958
+name: kassod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003959
+name: Hippophae tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003960
+name: dipterocarp tree
+synonym: "Dipterocarpaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003961
+name: Dekopon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003962
+name: cycad tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003963
+name: cupuassu tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003964
+name: cupressaceous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003965
+name: chitalpa tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003966
+name: chinquapin tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003967
+name: Casuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003968
+name: Ascomycota tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003969
+name: Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003970
+name: Allocasuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003971
+name: South-African Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003972
+name: African leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003973
+name: willow tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003974
+name: wild tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003976
+name: whitebark pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003977
+name: White spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003978
+name: white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003979
+name: white oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003980
+name: walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003981
+name: urban tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003982
+name: Ulmus nigra tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003983
+name: Ulmus Dodoens Elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003984
+name: turkey oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003985
+name: tung tree
+synonym: "tung oil tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003986
+name: tanoak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003987
+name: Talh tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003988
+name: sycamore tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003989
+name: sweet chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003990
+name: Swedish spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003991
+name: sudden oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003992
+name: stone pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003993
+name: silver birch
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003994
+name: silk oak
+synonym: "silk oak tree" EXACT []
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003995
+name: Sebertia acuminata
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003996
+name: scot pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003997
+name: riparian Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003998
+name: Rhodococcus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003999
+name: redwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004001
+name: radiata pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004002
+name: Quercus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004003
+name: pygmy tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004004
+name: prunus tree
+synonym: "Prunus spp. tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004005
+name: poplar tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004006
+name: ponderosa pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004007
+name: pomegranate tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004008
+name: pome tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004009
+name: poison oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004010
+name: pistachio tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004011
+name: pinyon pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004012
+name: persimmon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004013
+name: persian walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004014
+name: pepper tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004015
+name: pecan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004016
+name: Paulownia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004017
+name: palm tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004018
+name: ornamental tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004019
+name: ornamental Prunus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004020
+name: orchard tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004021
+name: Gingko tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004022
+name: nutmeg tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004023
+name: nutgall tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004024
+name: norway spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004025
+name: North American white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004026
+name: North American oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004027
+name: needled white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004028
+name: needle pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004029
+name: Monterey pine
+synonym: "insignis pine" EXACT []
+synonym: "radiata pine" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004030
+name: Mongolian pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004031
+name: medlar tree
+synonym: "Mespilus germanica" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004032
+name: Mediterranean oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004033
+name: Maritime pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004034
+name: mangrove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004035
+name: litchi tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004036
+name: laurel tree
+synonym: "Lauraceae tree" EXACT []
+synonym: "lauraceous tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004037
+name: Larix sibirica tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004038
+name: larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004039
+name: kraft pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004040
+name: Korean native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004041
+name: Korean lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004042
+name: Korean fir tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004043
+name: Korea spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004044
+name: kiwifruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004045
+name: khat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004046
+name: jujube tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004047
+name: Juglandaceae walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004048
+name: Japanese Yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004049
+name: Japanese larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004050
+name: jack pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004051
+name: Indian yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004052
+name: Indian oak tree
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004053
+name: Indian cork tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004054
+name: Iberian oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004055
+name: holm oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004056
+name: Himalayan pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004057
+name: hazelnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004058
+name: guava tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004059
+name: grapefruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004060
+name: Garry oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004061
+name: Garcinia schomdurgkiana Pierre tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004062
+name: evergreen oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004063
+name: European white elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004064
+name: European hackberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004065
+name: European elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004066
+name: eucalyptus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004067
+name: English oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004068
+name: Engelmann spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004069
+name: Emory oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004070
+name: Eastern cottonwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004071
+name: Dutch elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004072
+name: deciduous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004073
+name: cypress tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004074
+name: cotton tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004075
+name: Azerbaijani almond tree
+is_a: OBT:001402 ! almond tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004076
+name: coffee tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004077
+name: coconut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004078
+name: cocoa tree
+synonym: "chocolate tree" EXACT []
+synonym: "Theobroma cacao" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004079
+name: clove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004080
+name: clementine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004081
+name: chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004082
+name: Cherry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004083
+name: carob tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004084
+name: camellia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004085
+name: brazil nut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004086
+name: blueberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004087
+name: black oak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004088
+name: Bishop pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004090
+name: Betula tree
+synonym: "Betulaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004091
+name: Betula pendula tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004092
+name: beech tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004093
+name: banyan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004094
+name: avocado tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004095
+name: Austrian pine
+synonym: "Austrian pine tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004096
+name: Australian native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004097
+name: Australian native Grey Box tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004098
+name: Australian Hibiscus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004099
+name: Aspen tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004100
+name: argan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004101
+name: Alep pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004102
+name: ald tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004103
+name: acerola tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004104
+name: acacia tree
+synonym: "acacia" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004106
+name: orchad
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004107
+name: planthopper
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004108
+name: jumping plant lice
+synonym: "Psyllidae" NARROW []
+synonym: "psyllids" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004109
+name: sap-feeding insect
+synonym: "sap-sucking insect" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004110
+name: sentinel plant
+is_a: OBT:000912 ! terrestrial plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004111
+name: peony
+is_a: OBT:004110 ! sentinel plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004112
+name: piercing-sucking insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004113
+name: Myzus persicae
+synonym: "green peach aphid" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004114
+name: cabbage aphid
+synonym: "Brevicoryne brassicae" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004115
+name: phytophagous insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004116
+name: cotton boll worm
+synonym: "Helicoverpa armigera" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004117
+name: black cut worm
+synonym: "Agrotis ipsilon" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004118
+name: cotton leaf worm
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004119
+name: rice yellow stem borer
+synonym: "Scirpophaga incertulas" EXACT []
+is_a: OBT:001652 ! moth
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004120
+name: Asian citrus psyllid
+synonym: "Diaphorina citri" EXACT []
+is_a: OBT:004108 ! jumping plant lice
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004121
+name: vineyard
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004122
+name: Graphocephala versuta
+is_a: OBT:002248 ! sharpshooter
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004123
+name: xylem sap-feeding insect
+is_a: OBT:004109 ! sap-feeding insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:009115
+name: palm forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
diff --git a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo b/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
index 86297a0d..05d3f686 100644
--- a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000002
@@ -55,7 +54,7 @@ is_a: OBT:000002 ! microbial phenotype
 
 [Term]
 id: OBT:000024
-name: phenotypre wrt genetic
+name: phenotype wrt genetic
 is_a: OBT:000002 ! microbial phenotype
 
 [Term]
@@ -216,7 +215,7 @@ is_a: OBT:000021 ! phenotype wrt motility
 [Term]
 id: OBT:000118
 name: mutant
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000120
@@ -393,7 +392,7 @@ is_a: OBT:000017 ! phenotype wrt environment
 id: OBT:000169
 name: wild-type
 synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000172
@@ -2340,3 +2339,10 @@ name: chemolithoheterotroph
 synonym: "chemo lithoheterotroph " EXACT [TyDI:54334]
 is_a: OBT:002895 ! chemoheterotroph
 is_a: OBT:002896 ! chemolithotroph
+
+[Term]
+id: OBT:003614
+name: cord-shaped
+is_a: OBT:000386 ! phenotype wrt shape
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
diff --git a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo b/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
index ed2e6ac0..9a9716d4 100644
--- a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
+++ b/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
@@ -1,8 +1,7 @@
 format-version: 1.2
-date: 27:11:2019 14:34
+date: 25:02:2021 17:05
 saved-by: claire
 auto-generated-by: OBO-Edit 2.3.1
-default-namespace: file:/Users/claire/recherche/org/2019/BioNLP-OST19/OntoBiotope/def/OntoBiotope_BioNLP-OST-2019.obo
 
 [Term]
 id: OBT:000000
@@ -128,7 +127,7 @@ is_a: OBT:000002 ! microbial phenotype
 
 [Term]
 id: OBT:000024
-name: phenotypre wrt genetic
+name: phenotype wrt genetic
 is_a: OBT:000002 ! microbial phenotype
 
 [Term]
@@ -356,6 +355,7 @@ is_a: OBT:000006 ! artificial environment
 [Term]
 id: OBT:000067
 name: cultivated habitat
+synonym: "cultivated area" EXACT []
 is_a: OBT:000004 ! animal husbandry and agricultural habitat
 
 [Term]
@@ -631,7 +631,7 @@ is_a: OBT:000021 ! phenotype wrt motility
 [Term]
 id: OBT:000118
 name: mutant
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000119
@@ -906,7 +906,7 @@ is_a: OBT:000009 ! habitat wrt chemico-physical property
 id: OBT:000169
 name: wild-type
 synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotypre wrt genetic
+is_a: OBT:000024 ! phenotype wrt genetic
 
 [Term]
 id: OBT:000170
@@ -1210,7 +1210,7 @@ is_a: OBT:000156 ! subterrestrial habitat
 [Term]
 id: OBT:000226
 name: ceiling tile
-is_a: OBT:000098 ! household good
+is_a: OBT:003617 ! environmental surface
 
 [Term]
 id: OBT:000227
@@ -2105,7 +2105,7 @@ is_a: OBT:000094 ! food for human
 
 [Term]
 id: OBT:000398
-name: prothesis
+name: prosthesis
 is_a: OBT:000108 ! medical equipment
 
 [Term]
@@ -2152,6 +2152,7 @@ is_a: OBT:000093 ! fish pond
 id: OBT:000407
 name: respiratory tract
 synonym: "respiratory" RELATED [TyDI:55563]
+synonym: "respiratory airway" RELATED []
 synonym: "respiratory tree" RELATED [TyDI:55564]
 is_a: OBT:000039 ! animal part
 
@@ -2284,6 +2285,7 @@ is_a: OBT:000110 ! medical sample
 id: OBT:000432
 name: starter culture
 synonym: "dry starter" RELATED [TyDI:52942]
+synonym: "starter" EXACT []
 is_a: OBT:000113 ! microflora
 
 [Term]
@@ -2574,6 +2576,7 @@ is_a: OBT:000190 ! anaerobic bioreactor
 [Term]
 id: OBT:000488
 name: anaerobic sludge blanket reactor
+synonym: "UASB reactor" EXACT []
 is_a: OBT:000190 ! anaerobic bioreactor
 
 [Term]
@@ -2624,7 +2627,7 @@ is_a: OBT:000332 ! lesion
 [Term]
 id: OBT:000498
 name: auricular prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000499
@@ -2654,6 +2657,7 @@ is_a: OBT:000208 ! bathroom equipment
 [Term]
 id: OBT:000504
 name: bathtub
+synonym: "bath tub" EXACT []
 is_a: OBT:000208 ! bathroom equipment
 
 [Term]
@@ -2785,7 +2789,7 @@ is_a: OBT:000340 ! meat and bone meal
 [Term]
 id: OBT:000528
 name: bone-anchored prosthesis
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000529
@@ -2978,7 +2982,7 @@ is_a: OBT:000228 ! cellular shape phenotype
 id: OBT:000564
 name: cochlear prosthesis
 synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003645 ! ocular prosthesis
 
 [Term]
 id: OBT:000565
@@ -3014,7 +3018,7 @@ is_a: OBT:000240 ! commodity and primary derivative thereof
 [Term]
 id: OBT:000571
 name: compost
-is_a: OBT:000365 ! organic matter
+is_a: OBT:000585 ! dead matter
 
 [Term]
 id: OBT:000572
@@ -3083,6 +3087,7 @@ is_a: OBT:000194 ! animal farm
 [Term]
 id: OBT:000584
 name: dairy starter culture
+synonym: "dairy starter" EXACT []
 is_a: OBT:000432 ! starter culture
 
 [Term]
@@ -3120,8 +3125,8 @@ is_a: OBT:000313 ! host associated biofilm
 
 [Term]
 id: OBT:000591
-name: dental prothesis
-is_a: OBT:000398 ! prothesis
+name: dental prosthesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000592
@@ -3696,7 +3701,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000701
 name: laryngeal prosthetic device
-is_a: OBT:000398 ! prothesis
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000702
@@ -3798,11 +3803,13 @@ is_a: OBT:000364 ! organ
 [Term]
 id: OBT:000720
 name: maize feed
+synonym: "corn feed" NARROW []
 is_a: OBT:000229 ! cereal feed
 
 [Term]
 id: OBT:000721
 name: maize storage
+synonym: "corn storage" NARROW []
 is_a: OBT:000423 ! silo
 
 [Term]
@@ -3847,7 +3854,7 @@ is_a: OBT:000341 ! medical outfit
 
 [Term]
 id: OBT:000730
-name: membrane
+name: animal membrane
 is_a: OBT:000196 ! animal tissue
 
 [Term]
@@ -4135,7 +4142,7 @@ is_a: OBT:000371 ! oxidase activity
 [Term]
 id: OBT:000786
 name: pacemaker
-is_a: OBT:000398 ! prothesis
+is_a: OBT:003632 ! prosthetic cardiac device
 
 [Term]
 id: OBT:000787
@@ -4364,7 +4371,8 @@ is_a: OBT:000463 ! urogenital tract part
 [Term]
 id: OBT:000830
 name: prosthetic joint
-is_a: OBT:000398 ! prothesis
+synonym: "joint prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
 
 [Term]
 id: OBT:000831
@@ -4988,7 +4996,7 @@ is_a: OBT:000193 ! animal
 [Term]
 id: OBT:000947
 name: veterinary drug
-is_a: OBT:000261 ! drug
+is_a: OBT:003680 ! veterinary product
 
 [Term]
 id: OBT:000948
@@ -6270,6 +6278,7 @@ is_a: OBT:000684 ! industrial equipment
 [Term]
 id: OBT:001190
 name: maize silage
+synonym: "corn silage" NARROW []
 is_a: OBT:000871 ! silage
 
 [Term]
@@ -6334,7 +6343,7 @@ is_a: OBT:000816 ! plant tissue
 [Term]
 id: OBT:001202
 name: mesentery
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001203
@@ -6427,7 +6436,7 @@ is_a: OBT:000710 ! lining
 id: OBT:001219
 name: mucous membrane
 synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001220
@@ -6608,7 +6617,7 @@ is_a: OBT:000642 ! gastrointestinal tract part
 [Term]
 id: OBT:001253
 name: peritoneum
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001254
@@ -7161,6 +7170,7 @@ is_a: OBT:000529 ! broncho-pulmonary segment
 id: OBT:001359
 name: treated wood
 is_a: OBT:000586 ! dead wood
+is_a: OBT:003742 ! wood waste
 
 [Term]
 id: OBT:001360
@@ -7307,7 +7317,7 @@ is_a: OBT:000809 ! pigmented
 [Term]
 id: OBT:001387
 name: yolk sac
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:001388
@@ -7600,6 +7610,7 @@ is_a: OBT:001005 ! biofilm phenotype
 [Term]
 id: OBT:001445
 name: birch
+synonym: "birch tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -8108,11 +8119,6 @@ id: OBT:001544
 name: eosinophil
 is_a: OBT:001134 ! granulocyte
 
-[Term]
-id: OBT:001545
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-
 [Term]
 id: OBT:001546
 name: fermented food
@@ -8181,6 +8187,7 @@ is_a: OBT:001097 ! factory
 [Term]
 id: OBT:001558
 name: food processing waste
+synonym: "food residue" RELATED []
 is_a: OBT:001157 ! industrial organic waste
 
 [Term]
@@ -8228,7 +8235,8 @@ is_a: OBT:001114 ! food rind
 [Term]
 id: OBT:001567
 name: fruit tree
-is_a: OBT:001360 ! tree
+comment: horticole meaning
+is_a: OBT:002699 ! cultivated plant
 
 [Term]
 id: OBT:001568
@@ -8740,6 +8748,7 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 [Term]
 id: OBT:001666
 name: oak
+synonym: "oak tree" EXACT []
 is_a: OBT:001360 ! tree
 
 [Term]
@@ -8999,7 +9008,7 @@ is_a: OBT:001257 ! plankton
 [Term]
 id: OBT:001715
 name: pine forest
-is_a: OBT:001119 ! forest
+is_a: OBT:003881 ! conifer forest
 
 [Term]
 id: OBT:001716
@@ -9013,8 +9022,9 @@ is_a: OBT:001232 ! nut and primary derivative thereof
 
 [Term]
 id: OBT:001718
-name: plant residue
-is_a: OBT:001258 ! plant material
+name: agricultural plant residue
+synonym: "agricultural plant waste" NARROW []
+is_a: OBT:000478 ! agricultural waste
 
 [Term]
 id: OBT:001719
@@ -9043,7 +9053,7 @@ is_a: OBT:001132 ! grain and primary derivative thereof
 
 [Term]
 id: OBT:001724
-name: potato
+name: potato plant
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -9458,8 +9468,8 @@ is_a: OBT:001045 ! confectionery
 
 [Term]
 id: OBT:001803
-name: sugar-beet
-synonym: "betroot" EXACT [TyDI:49625]
+name: sugar-beet plant
+synonym: "betroot plant" EXACT [TyDI:49625]
 is_a: OBT:001362 ! tuber
 
 [Term]
@@ -9536,7 +9546,8 @@ is_a: OBT:001159 ! industrial sludge
 
 [Term]
 id: OBT:001818
-name: textile industry
+name: textile mill
+synonym: "textile factory" NARROW []
 is_a: OBT:001097 ! factory
 
 [Term]
@@ -10394,8 +10405,9 @@ is_a: OBT:001621 ! livestock barn
 
 [Term]
 id: OBT:001988
-name: dairy industry
-synonym: "milk industry" RELATED [TyDI:55159]
+name: dairy processing plant
+synonym: "dairy factory" EXACT []
+synonym: "milk processing factory" RELATED [TyDI:55159]
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -10666,7 +10678,7 @@ is_a: OBT:001446 ! bird
 
 [Term]
 id: OBT:002039
-name: food fermentation industry
+name: food fermentation factory
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -10846,7 +10858,7 @@ is_a: OBT:001821 ! tick
 [Term]
 id: OBT:002073
 name: hay
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002074
@@ -10914,7 +10926,7 @@ is_a: OBT:001557 ! food processing factory
 id: OBT:002086
 name: industrial bakery
 synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:003759 ! bakery
 
 [Term]
 id: OBT:002087
@@ -11131,7 +11143,7 @@ is_a: OBT:001802 ! sugar confectionery
 
 [Term]
 id: OBT:002129
-name: meat industry
+name: meat processing plant
 is_a: OBT:001557 ! food processing factory
 
 [Term]
@@ -11442,7 +11454,7 @@ is_a: OBT:001717 ! pistachio and primary derivative thereof
 [Term]
 id: OBT:002190
 name: plant cutting
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002191
@@ -11622,7 +11634,7 @@ is_a: OBT:001744 ! rice based dish
 [Term]
 id: OBT:002225
 name: rice-plant residue
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002226
@@ -11757,7 +11769,7 @@ id: OBT:002251
 name: slaughter plant
 synonym: "abattoir" RELATED [TyDI:50262]
 synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:001557 ! food processing factory
+is_a: OBT:002129 ! meat processing plant
 
 [Term]
 id: OBT:002252
@@ -11864,7 +11876,7 @@ is_a: OBT:001556 ! food fermentation equipment
 [Term]
 id: OBT:002271
 name: straw
-is_a: OBT:001718 ! plant residue
+is_a: OBT:001718 ! agricultural plant residue
 
 [Term]
 id: OBT:002272
@@ -12400,7 +12412,7 @@ is_a: OBT:002018 ! environmental water with chemical property
 [Term]
 id: OBT:002372
 name: brewery
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:002373
@@ -12622,7 +12634,7 @@ is_a: OBT:002174 ! pastry product
 [Term]
 id: OBT:002414
 name: creamery
-is_a: OBT:001988 ! dairy industry
+is_a: OBT:001988 ! dairy processing plant
 
 [Term]
 id: OBT:002415
@@ -13150,6 +13162,7 @@ is_a: OBT:002126 ! marine fish meat
 [Term]
 id: OBT:002513
 name: maize
+synonym: "corn" NARROW []
 is_a: OBT:002120 ! maize and primary derivative thereof
 
 [Term]
@@ -14639,7 +14652,7 @@ name: endothelium
 synonym: "endothelial" RELATED [TyDI:52445]
 synonym: "vascular endothelium" EXACT [TyDI:52444]
 is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:002790
@@ -15335,6 +15348,7 @@ is_a: OBT:000710 ! lining
 [Term]
 id: OBT:002914
 name: maize plant
+synonym: "corn plant" NARROW []
 is_a: OBT:002771 ! cereal crop
 
 [Term]
@@ -15752,6 +15766,7 @@ name: hotspring
 synonym: "hot spring" EXACT [TyDI:49581]
 is_a: OBT:000625 ! extreme high temperature environment
 is_a: OBT:001333 ! spring
+is_a: OBT:002019 ! environmental water with physical property
 
 [Term]
 id: OBT:002991
@@ -16371,7 +16386,7 @@ is_a: OBT:001632 ! market garden plant
 
 [Term]
 id: OBT:003098
-name: gum margin
+name: gingival margin
 is_a: OBT:003055 ! gum tissue
 
 [Term]
@@ -17073,7 +17088,7 @@ id: OBT:003221
 name: peritrophic membrane
 is_a: OBT:000200 ! arthropod part
 is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! membrane
+is_a: OBT:000730 ! animal membrane
 
 [Term]
 id: OBT:003222
@@ -17250,8 +17265,8 @@ is_a: OBT:002055 ! fungi as food
 [Term]
 id: OBT:003251
 name: cheese factory
-is_a: OBT:001988 ! dairy industry
-is_a: OBT:002039 ! food fermentation industry
+is_a: OBT:001988 ! dairy processing plant
+is_a: OBT:002039 ! food fermentation factory
 
 [Term]
 id: OBT:003252
@@ -17337,6 +17352,7 @@ is_a: OBT:003203 ! heavy metal contaminated soil
 id: OBT:003266
 name: mine waste water
 synonym: "mine wastewater" EXACT [TyDI:51583]
+synonym: "mine water" EXACT []
 is_a: OBT:001212 ! mine waste
 is_a: OBT:002754 ! waste water
 
@@ -18538,7 +18554,7 @@ is_a: OBT:003458 ! semi soft cheese
 
 [Term]
 id: OBT:003475
-name: Granular
+name: Granular cheese
 is_a: OBT:003450 ! hard cheese
 
 [Term]
@@ -19246,3 +19262,3568 @@ synonym: "tejuíno" EXACT [TyDI:51685]
 is_a: OBT:003410 ! corn beverage
 is_a: OBT:003596 ! fermented juice
 
+[Term]
+id: OBT:003602
+name: airway epithelium
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003603
+name: chicken breast meat
+is_a: OBT:002394 ! chicken meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003604
+name: turkey breast meat
+is_a: OBT:002631 ! turkey meat
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003605
+name: rice bran
+is_a: OBT:001458 ! bran
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003606
+name: lacrimal sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003607
+name: conjunctival sac
+is_a: OBT:000277 ! eye part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003608
+name: aneurysmal sac
+synonym: "aneurysm sac" EXACT []
+synonym: "aortic sac" EXACT []
+is_a: OBT:000231 ! circulatory system part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003609
+name: abdominal air sac
+synonym: "air sac" EXACT []
+synonym: "thoracic air sac" EXACT []
+is_a: OBT:000408 ! respiratory tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003610
+name: hernial sac
+is_a: OBT:000039 ! animal part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003611
+name: umbilical cord
+is_a: OBT:000463 ! urogenital tract part
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003612
+name: umbilical cord blood
+is_a: OBT:000521 ! blood
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003613
+name: vocal cord
+is_a: OBT:000529 ! broncho-pulmonary segment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003614
+name: cord-shaped
+is_a: OBT:000386 ! phenotype wrt shape
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003615
+name: box lunch
+is_a: OBT:000788 ! packed lunch
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003617
+name: environmental surface
+is_a: OBT:000006 ! artificial environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003618
+name: ceramic tile
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003619
+name: ceramic wall tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003620
+name: ceramic roofing tile
+is_a: OBT:003618 ! ceramic tile
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003621
+name: stainless steel surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003622
+name: PCV surface
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003623
+name: plasticized PVC
+synonym: "PVC plastic" NARROW []
+is_a: OBT:003622 ! PCV surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003624
+name: PVC film
+is_a: OBT:000787 ! packaging
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003625
+name: sealed concrete
+is_a: OBT:003617 ! environmental surface
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003626
+name: bamboo cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003627
+name: wood Cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003628
+name: plastic cutting board
+is_a: OBT:000582 ! cutting board
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003629
+name: voice prosthesis
+is_a: OBT:003630 ! tracheoesophageal prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003630
+name: tracheoesophageal prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003631
+name: silicone rubber voice prosthesis
+is_a: OBT:003629 ! voice prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003632
+name: prosthetic cardiac device
+synonym: "intracardiac prosthesis" NARROW []
+synonym: "prosthetic cardiovascular device" NARROW []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003633
+name: prosthetic heart valve
+synonym: "heart valve prosthesis" NARROW []
+synonym: "prosthetic valve" NARROW []
+synonym: "valvular prosthesis" NARROW []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003634
+name: mitral valve prosthesis
+synonym: "mitral prosthesis" EXACT []
+is_a: OBT:003633 ! prosthetic heart valve
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003635
+name: aortic prosthetic valve
+synonym: "aortic valve prosthesis" EXACT []
+synonym: "arterial prosthesis" EXACT []
+is_a: OBT:003632 ! prosthetic cardiac device
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003636
+name: orthopedic prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003637
+name: othopedic implant
+is_a: OBT:003636 ! orthopedic prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003638
+name: hip prosthesis
+synonym: "prosthetic hip joint" EXACT []
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003639
+name: femoral prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003640
+name: knee prosthesis
+is_a: OBT:000830 ! prosthetic joint
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003641
+name: shoulder prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003642
+name: cranial prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003643
+name: penile prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003644
+name: testicular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003645
+name: ocular prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003646
+name: prosthetic eye
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003647
+name: iris prosthesis
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003648
+name: orbital implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003649
+name: cochlear implant
+is_a: OBT:003645 ! ocular prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003650
+name: dental implant
+is_a: OBT:000591 ! dental prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003651
+name: palatal obturator prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003652
+name: breast prosthesis
+synonym: "mammary prosthesis" EXACT []
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003653
+name: breast implant
+is_a: OBT:003652 ! breast prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003654
+name: suction-socket prosthesis
+is_a: OBT:000398 ! prosthesis
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003655
+name: granular sludge
+is_a: OBT:001523 ! digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003656
+name: aerobic granular sludge
+is_a: OBT:001861 ! anaerobic digester sludge
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003657
+name: aerobic granular sludge reactor
+synonym: "AGS reactor" EXACT []
+is_a: OBT:000180 ! aerobic bioreactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003658
+name: granular sludge bed reactor
+synonym: "EGSB reactor" EXACT []
+is_a: OBT:000488 ! anaerobic sludge blanket reactor
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003659
+name: public swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003660
+name: indoor swimming bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003661
+name: shower bath
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003662
+name: public bath
+is_a: OBT:002203 ! public bathing facility
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003663
+name: traditional public bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003664
+name: bath basin
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003665
+name: thermal bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003666
+name: thermal saline bath
+is_a: OBT:002592 ! saline water
+is_a: OBT:003665 ! thermal bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003667
+name: mineral bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003668
+name: spa bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003669
+name: seawater bath
+is_a: OBT:003105 ! marine water
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003670
+name: freshwater bath
+is_a: OBT:002455 ! freshwater
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003671
+name: open air bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003672
+name: spring bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003673
+name: hot water bath
+is_a: OBT:003662 ! public bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003674
+name: hot spring bath
+is_a: OBT:002990 ! hotspring
+is_a: OBT:003673 ! hot water bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003675
+name: hot spring spa bath
+is_a: OBT:003674 ! hot spring bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003676
+name: bath sponge
+is_a: OBT:000208 ! bathroom equipment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003677
+name: bath tub heating
+is_a: OBT:000671 ! home heating system
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003678
+name: antiseptic bath
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003679
+name: chlorhexidine bath
+is_a: OBT:003678 ! antiseptic bath
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003680
+name: veterinary product
+is_a: OBT:000011 ! medical environment
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003681
+name: insecticide bath
+is_a: OBT:003680 ! veterinary product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003682
+name: antiseptic shower
+is_a: OBT:000109 ! medical product
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003683
+name: dyeing bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003684
+name: skin tannery bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003685
+name: bleach bath
+is_a: OBT:000322 ! industrial chemical
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003689
+name: mango tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003690
+name: lemon tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003691
+name: peach tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003692
+name: apricot tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003693
+name: quince tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003694
+name: cherry tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003695
+name: khaki tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003696
+name: lime tree
+is_a: OBT:001567 ! fruit tree
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T18:51:57Z
+
+[Term]
+id: OBT:003697
+name: carrot plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003698
+name: broccoli plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003699
+name: brussel sprout plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003700
+name: chinese cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003701
+name: collard green plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003702
+name: head cabbage plant
+is_a: OBT:001391 ! Brassica
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003703
+name: shallot plant
+is_a: OBT:001389 ! Allium
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003704
+name: fruiting vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003705
+name: courgette plant
+synonym: "zucchini plant" EXACT []
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003706
+name: cucumber plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003707
+name: gherkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003708
+name: melon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003709
+name: pumpkin plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003710
+name: sweet pepper plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003711
+name: watermelon plant
+is_a: OBT:003704 ! fruiting vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003712
+name: leafy vegetable plant
+is_a: OBT:001632 ! market garden plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003713
+name: celery plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003714
+name: spinach plant
+is_a: OBT:003712 ! leafy vegetable plant
+created_by: Claire_Nedellec
+creation_date: 2020-10-27T12:51:57Z
+
+[Term]
+id: OBT:003715
+name: table water
+is_a: OBT:001530 ! drinking water
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003716
+name: garment factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003717
+name: dyeing factory
+is_a: OBT:001818 ! textile mill
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003718
+name: traditional Chinese fermented cabbage
+is_a: OBT:002321 ! Chinese cabbage
+is_a: OBT:003096 ! fermented vegetable product
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003719
+name: nasal swab
+is_a: OBT:001228 ! nasal secretion
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003720
+name: rum factory
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003721
+name: whisky distillery
+is_a: OBT:002039 ! food fermentation factory
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003722
+name: liquor
+is_a: OBT:001397 ! alcoholic drink
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003723
+name: udder
+is_a: OBT:000723 ! mammalian part
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003724
+name: lactic starter
+is_a: OBT:000584 ! dairy starter culture
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003726
+name: plant residue from food processing
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003727
+name: grape pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003728
+name: apple pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003729
+name: olive pomace
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003730
+name: grape must
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003731
+name: sugarcane bagasse
+synonym: "sugar cane bagasse" EXACT []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003732
+name: agave bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003733
+name: citrus bagasse
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003734
+name: soy bran
+is_a: OBT:000038 ! animal feed
+created_by: Claire_Nedellec
+creation_date: 2020-10-30T12:51:57Z
+
+[Term]
+id: OBT:003735
+name: palm kernel press cake
+synonym: "residue from palm oil extraction" NARROW []
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003736
+name: sugar beet pressed pulp
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003737
+name: cranberry press cake
+is_a: OBT:001558 ! food processing waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003738
+name: forage residue
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003739
+name: cotton plant waste
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003740
+name: cottonseed hull
+is_a: OBT:001718 ! agricultural plant residue
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003741
+name: olive press cake
+is_a: OBT:003726 ! plant residue from food processing
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003742
+name: wood waste
+is_a: OBT:000467 ! waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003743
+name: sawdust
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003744
+name: waste house wood
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003745
+name: construction wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003746
+name: demolition wood waste
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003747
+name: hazardous industrial waste
+is_a: OBT:000685 ! industrial waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003748
+name: agricultural woody waste
+is_a: OBT:000478 ! agricultural waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003749
+name: wood waste fiber
+is_a: OBT:003742 ! wood waste
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003750
+name: transport structure
+is_a: OBT:000162 ! transport equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003751
+name: pallet
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003752
+name: shipping container
+is_a: OBT:003750 ! transport structure
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003753
+name: wooden pallet
+is_a: OBT:003751 ! pallet
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003756
+name: wood barrel
+is_a: OBT:000434 ! storage equipment
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003757
+name: oak barrel
+is_a: OBT:003756 ! wood barrel
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003759
+name: bakery
+is_a: OBT:001557 ! food processing factory
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003760
+name: traditional bakery
+is_a: OBT:003759 ! bakery
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003761
+name: traditional dairy
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2020-11-03T10:10:57Z
+
+[Term]
+id: OBT:003762
+name: dairy farm
+is_a: OBT:001988 ! dairy processing plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003763
+name: snowpack
+is_a: OBT:000881 ! snow
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003764
+name: conifer needle
+is_a: OBT:000807 ! phylloplane part
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003765
+name: agricultural fence
+is_a: OBT:001183 ! livestock habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003766
+name: ungulate
+is_a: OBT:002078 ! herbivore
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003767
+name: biome type forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003768
+name: alpine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003769
+name: tropical rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003770
+name: arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003771
+name: boreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003772
+name: coastal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003773
+name: cooler rain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003774
+name: dune forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003775
+name: equatorial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003776
+name: montane forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003777
+name: hemiboreal forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003778
+name: high altitude forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003779
+name: humid lakeland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003780
+name: low mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003781
+name: subtropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003782
+name: taiga forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003783
+name: lowland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003784
+name: marshy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003785
+name: mountain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003786
+name: neotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003787
+name: paleotropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003788
+name: savannah - forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003789
+name: subalpine forest
+synonym: "sub-alpine forest" EXACT []
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003790
+name: sub-Antarctic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003791
+name: warm sub-tropical forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003792
+name: dry forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003793
+name: semi - arid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003794
+name: semiarid temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003795
+name: hill forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003796
+name: hot forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003797
+name: humid forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003798
+name: inland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003799
+name: moist forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003800
+name: plain forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003801
+name: pluvial forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003802
+name: riverbank forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003803
+name: riverine forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003804
+name: submerged forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003805
+name: temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003806
+name: underwater forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003807
+name: upland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003808
+name: volcanic forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003809
+name: warm - temperate forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003810
+name: wet forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003811
+name: wildland forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003812
+name: drained forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003813
+name: soddy forest
+is_a: OBT:003767 ! biome type forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003814
+name: natural and managed forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T12:10:57Z
+
+[Term]
+id: OBT:003815
+name: natural forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003816
+name: virgin forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003817
+name: uncontrolled forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003818
+name: undisturbed forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003819
+name: unmanaged forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003820
+name: unpolluted forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003821
+name: preserved forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003822
+name: protected forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003823
+name: native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003824
+name: intact forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003825
+name: primary forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003826
+name: primeval forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003827
+name: pristine area of native forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003828
+name: pristine forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003829
+name: non-burnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003830
+name: unburnt forest
+is_a: OBT:003815 ! natural forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003831
+name: managed forest
+is_a: OBT:003814 ! natural and managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003832
+name: man - made forest system
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003833
+name: municipal forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003834
+name: park forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003836
+name: periurban forest
+synonym: "peri-urban" EXACT []
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003837
+name: plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003838
+name: recreational forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003839
+name: reserve forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003840
+name: rural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003841
+name: semi-natural forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003842
+name: suburban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003843
+name: urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003844
+name: village-adjacent forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003845
+name: village forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003846
+name: wood forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003847
+name: second-growth forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003848
+name: secondary forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003849
+name: early successional forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003850
+name: burnt forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003851
+name: artificial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003852
+name: commercial forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003853
+name: commercial plantation forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003854
+name: community forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003855
+name: disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003856
+name: disturbed urban forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003857
+name: historical forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003858
+name: human disturbed forest
+is_a: OBT:003831 ! managed forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:08:57Z
+
+[Term]
+id: OBT:003859
+name: old forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003860
+name: mature forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003861
+name: mature forest of high conservation value
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003862
+name: mature old-growth forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003863
+name: young forest
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003864
+name: forest of given species
+is_a: OBT:001119 ! forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003865
+name: alder forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003866
+name: angiosperm-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003867
+name: arboreal forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003868
+name: argan forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003869
+name: aspen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003870
+name: beach forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003871
+name: beech forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003872
+name: beech-dominated forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003873
+name: birch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003874
+name: boreonemoral forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003875
+name: bosque forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003876
+name: broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003877
+name: broadleaf forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003878
+name: Cercocarpus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003879
+name: chestnut forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003880
+name: cloud forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003881
+name: conifer forest
+synonym: "coniferous forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003883
+name: coppice forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003884
+name: cypress forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003885
+name: deciduous forest
+synonym: "deciduous specie forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003886
+name: deciduous dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003888
+name: herb-rich coniferous forest
+is_a: OBT:003881 ! conifer forest
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003890
+name: dipterocarp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003892
+name: evergreen broad-leaved forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003893
+name: forest with dominant vegetation
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003894
+name: hardwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003896
+name: holm-oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003897
+name: kelp forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003898
+name: larch forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003899
+name: lucidophyllous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003900
+name: mangrove forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003901
+name: maple forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003902
+name: maso bamboo forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003903
+name: hemlock fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003904
+name: amabilis fir forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003906
+name: monodominant forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003907
+name: monospecific forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003908
+name: spruce forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003909
+name: Nothofagaceae forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003910
+name: Nothofagus forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003911
+name: oak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003912
+name: oak-hickory forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003914
+name: ombrophilous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003916
+name: papyrifera forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003917
+name: perennial forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003918
+name: riparian forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003919
+name: pure forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003920
+name: red pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003921
+name: redwood forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003922
+name: riparian woodland
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003923
+name: poplar forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003924
+name: sclerophyll forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003925
+name: seasonal dry tropical forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003926
+name: scrub forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003927
+name: semi-evergreen forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003928
+name: semideciduous forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003929
+name: stone pine forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003931
+name: tanoak forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003932
+name: xeric forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003933
+name: xerophytic forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003934
+name: mix forest
+synonym: "mixed forest" EXACT []
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
+[Term]
+id: OBT:003935
+name: papilionoid legume tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003936
+name: leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003937
+name: tulip tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003938
+name: tea-oil tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003939
+name: tea plant
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003940
+name: Syzygiumcordatum tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003941
+name: shea butter tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003942
+name: rubber tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003943
+name: riparian tree specie
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003944
+name: Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003945
+name: Prosopis tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003946
+name: peepal tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003947
+name: Pandanus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003948
+name: pacara earpod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003949
+name: Olea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003950
+name: Nothofagus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003951
+name: mopane tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003952
+name: Masson pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003953
+name: manuka tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003954
+name: loquat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003955
+name: lodgepole pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003956
+name: lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003957
+name: Katsura tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003958
+name: kassod tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003959
+name: Hippophae tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003960
+name: dipterocarp tree
+synonym: "Dipterocarpaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003961
+name: Dekopon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003962
+name: cycad tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003963
+name: cupuassu tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003964
+name: cupressaceous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003965
+name: chitalpa tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003966
+name: chinquapin tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003967
+name: Casuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003968
+name: Ascomycota tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003969
+name: Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003970
+name: Allocasuarina tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003971
+name: South-African Protea tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003972
+name: African leguminous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003973
+name: willow tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003974
+name: wild tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003976
+name: whitebark pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003977
+name: White spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003978
+name: white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003979
+name: white oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003980
+name: walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003981
+name: urban tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003982
+name: Ulmus nigra tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003983
+name: Ulmus Dodoens Elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003984
+name: turkey oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003985
+name: tung tree
+synonym: "tung oil tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003986
+name: tanoak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003987
+name: Talh tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003988
+name: sycamore tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003989
+name: sweet chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003990
+name: Swedish spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003991
+name: sudden oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003992
+name: stone pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003993
+name: silver birch
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003994
+name: silk oak
+synonym: "silk oak tree" EXACT []
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003995
+name: Sebertia acuminata
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003996
+name: scot pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003997
+name: riparian Alnus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003998
+name: Rhodococcus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:003999
+name: redwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004001
+name: radiata pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004002
+name: Quercus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004003
+name: pygmy tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004004
+name: prunus tree
+synonym: "Prunus spp. tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004005
+name: poplar tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004006
+name: ponderosa pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004007
+name: pomegranate tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004008
+name: pome tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004009
+name: poison oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004010
+name: pistachio tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004011
+name: pinyon pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004012
+name: persimmon tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004013
+name: persian walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004014
+name: pepper tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004015
+name: pecan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004016
+name: Paulownia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004017
+name: palm tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004018
+name: ornamental tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004019
+name: ornamental Prunus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004020
+name: orchard tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004021
+name: Gingko tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004022
+name: nutmeg tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004023
+name: nutgall tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004024
+name: norway spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004025
+name: North American white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004026
+name: North American oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004027
+name: needled white pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004028
+name: needle pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004029
+name: Monterey pine
+synonym: "insignis pine" EXACT []
+synonym: "radiata pine" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004030
+name: Mongolian pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004031
+name: medlar tree
+synonym: "Mespilus germanica" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004032
+name: Mediterranean oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004033
+name: Maritime pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004034
+name: mangrove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004035
+name: litchi tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004036
+name: laurel tree
+synonym: "Lauraceae tree" EXACT []
+synonym: "lauraceous tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004037
+name: Larix sibirica tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004038
+name: larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004039
+name: kraft pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004040
+name: Korean native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004041
+name: Korean lacquer tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004042
+name: Korean fir tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004043
+name: Korea spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004044
+name: kiwifruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004045
+name: khat tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004046
+name: jujube tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004047
+name: Juglandaceae walnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004048
+name: Japanese Yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004049
+name: Japanese larch tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004050
+name: jack pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004051
+name: Indian yew tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004052
+name: Indian oak tree
+is_a: OBT:001666 ! oak
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004053
+name: Indian cork tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004054
+name: Iberian oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004055
+name: holm oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004056
+name: Himalayan pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004057
+name: hazelnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004058
+name: guava tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004059
+name: grapefruit tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004060
+name: Garry oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004061
+name: Garcinia schomdurgkiana Pierre tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004062
+name: evergreen oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004063
+name: European white elm
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004064
+name: European hackberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004065
+name: European elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004066
+name: eucalyptus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004067
+name: English oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004068
+name: Engelmann spruce
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004069
+name: Emory oak
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004070
+name: Eastern cottonwood tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004071
+name: Dutch elm
+is_a: OBT:001542 ! elm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004072
+name: deciduous tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004073
+name: cypress tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004074
+name: cotton tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004075
+name: Azerbaijani almond tree
+is_a: OBT:001402 ! almond tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004076
+name: coffee tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004077
+name: coconut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004078
+name: cocoa tree
+synonym: "chocolate tree" EXACT []
+synonym: "Theobroma cacao" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004079
+name: clove tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004080
+name: clementine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004081
+name: chestnut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004082
+name: Cherry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004083
+name: carob tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004084
+name: camellia tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004085
+name: brazil nut tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004086
+name: blueberry tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004087
+name: black oak tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004088
+name: Bishop pine
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004090
+name: Betula tree
+synonym: "Betulaceae tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004091
+name: Betula pendula tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004092
+name: beech tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004093
+name: banyan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004094
+name: avocado tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004095
+name: Austrian pine
+synonym: "Austrian pine tree" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004096
+name: Australian native pine tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004097
+name: Australian native Grey Box tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004098
+name: Australian Hibiscus tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004099
+name: Aspen tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004100
+name: argan tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004101
+name: Alep pine
+is_a: OBT:002187 ! pine
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004102
+name: ald tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004103
+name: acerola tree
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004104
+name: acacia tree
+synonym: "acacia" EXACT []
+is_a: OBT:001360 ! tree
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T13:37:57Z
+
+[Term]
+id: OBT:004106
+name: orchad
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004107
+name: planthopper
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004108
+name: jumping plant lice
+synonym: "Psyllidae" NARROW []
+synonym: "psyllids" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004109
+name: sap-feeding insect
+synonym: "sap-sucking insect" NARROW []
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004110
+name: sentinel plant
+is_a: OBT:000912 ! terrestrial plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004111
+name: peony
+is_a: OBT:004110 ! sentinel plant
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004112
+name: piercing-sucking insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004113
+name: Myzus persicae
+synonym: "green peach aphid" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004114
+name: cabbage aphid
+synonym: "Brevicoryne brassicae" EXACT []
+is_a: OBT:001428 ! aphid
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004115
+name: phytophagous insect
+is_a: OBT:001163 ! insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004116
+name: cotton boll worm
+synonym: "Helicoverpa armigera" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004117
+name: black cut worm
+synonym: "Agrotis ipsilon" EXACT []
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004118
+name: cotton leaf worm
+is_a: OBT:001385 ! worm
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004119
+name: rice yellow stem borer
+synonym: "Scirpophaga incertulas" EXACT []
+is_a: OBT:001652 ! moth
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004120
+name: Asian citrus psyllid
+synonym: "Diaphorina citri" EXACT []
+is_a: OBT:004108 ! jumping plant lice
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004121
+name: vineyard
+is_a: OBT:000067 ! cultivated habitat
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004122
+name: Graphocephala versuta
+is_a: OBT:002248 ! sharpshooter
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:004123
+name: xylem sap-feeding insect
+is_a: OBT:004109 ! sap-feeding insect
+created_by: Claire_Nedellec
+creation_date: 2021-02-18T17:35:57Z
+
+[Term]
+id: OBT:009115
+name: palm forest
+is_a: OBT:003864 ! forest of given species
+created_by: Claire_Nedellec
+creation_date: 2021-02-16T17:38:57Z
+
-- 
GitLab


From 0e9da0031753389bc39080b063ba2177af63f438 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 12:49:07 +0000
Subject: [PATCH 61/64] Delete BioNLP-OST+EnovFood-Habitat.obo

---
 ancillaries/BioNLP-OST+EnovFood-Habitat.obo | 20478 ------------------
 1 file changed, 20478 deletions(-)
 delete mode 100644 ancillaries/BioNLP-OST+EnovFood-Habitat.obo

diff --git a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo b/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
deleted file mode 100644
index 5ac41ce6..00000000
--- a/ancillaries/BioNLP-OST+EnovFood-Habitat.obo
+++ /dev/null
@@ -1,20478 +0,0 @@
-format-version: 1.2
-date: 25:02:2021 17:05
-saved-by: claire
-auto-generated-by: OBO-Edit 2.3.1
-
-[Term]
-id: OBT:000001
-name: microbial habitat
-
-[Term]
-id: OBT:000003
-name: animal habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000004
-name: animal husbandry and agricultural habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000005
-name: aquaculture habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000006
-name: artificial environment
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000007
-name: experimental medium
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000008
-name: food
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000009
-name: habitat wrt chemico-physical property
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000010
-name: living organism
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000011
-name: medical environment
-synonym: "clinical" RELATED [TyDI:52464]
-synonym: "nosocomial" RELATED [TyDI:52463]
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000012
-name: microorganism associated habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000013
-name: natural environment habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000014
-name: part of living organism
-synonym: "host part" RELATED [TyDI:52452]
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000026
-name: planet
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000027
-name: Earth
-is_a: OBT:000026 ! planet
-
-[Term]
-id: OBT:000028
-name: L-( null )-tartrate enriched soil
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000030
-name: aerosol
-synonym: "aerosolized" RELATED [TyDI:53259]
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000031
-name: agar
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000032
-name: agricultural equipment
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000033
-name: agricultural input
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000034
-name: agricultural product
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000035
-name: agricultural species
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000038
-name: animal feed
-synonym: "animal food" RELATED [TyDI:52402]
-synonym: "zoo animal's food" RELATED [TyDI:52401]
-is_a: OBT:000008 ! food
-
-[Term]
-id: OBT:000039
-name: animal part
-synonym: "animal host part" RELATED [TyDI:53074]
-synonym: "body part" RELATED [TyDI:53075]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000041
-name: antibiotic-containing media
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000043
-name: apiary
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000044
-name: aquaculture equipment
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000045
-name: aquaculture farm
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000046
-name: aquaculture pond
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000047
-name: aquatic environment
-synonym: "aquatic" RELATED [TyDI:53034]
-synonym: "aquatic habitat" RELATED [TyDI:53033]
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000048
-name: area with climate property
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000049
-name: area with epidemiologic property
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000050
-name: artificial water environment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000052
-name: atmosphere part
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000054
-name: biofilm
-synonym: "microbial slime" RELATED [TyDI:53290]
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000056
-name: bioreactor
-synonym: "biofilm reactor" EXACT []
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000058
-name: bovine serum
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000059
-name: breeding site
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000061
-name: cell
-synonym: "cellular" EXACT [TyDI:53156]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000062
-name: cell culture
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000066
-name: constructed habitat
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000067
-name: cultivated habitat
-synonym: "cultivated area" EXACT []
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000071
-name: endolython
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000073
-name: endopelon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000074
-name: endophyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000076
-name: endopsammon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000077
-name: endozoon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000078
-name: environment wrt oxygen level
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000079
-name: environmental matter
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000081
-name: epilython
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000083
-name: epipelon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000085
-name: epipsammon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000087
-name: epixylon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000088
-name: epizoon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000089
-name: eukaryote host
-synonym: "eukaryote" RELATED [TyDI:53285]
-synonym: "eukaryotic" RELATED [TyDI:53283]
-synonym: "eukaryotic host" EXACT [TyDI:53284]
-synonym: "host" RELATED [TyDI:53282]
-is_a: OBT:000010 ! living organism
-
-[Term]
-id: OBT:000090
-name: extreme environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000091
-name: farm
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000092
-name: field
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000093
-name: fish pond
-synonym: "fish culture pond" EXACT [TyDI:53118]
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000094
-name: food for human
-synonym: "agro-alimentary environment" EXACT [TyDI:53274]
-synonym: "alimentary" RELATED [TyDI:53273]
-synonym: "food product" EXACT [TyDI:53272]
-synonym: "foodborne" RELATED [TyDI:53275]
-is_a: OBT:000008 ! food
-
-[Term]
-id: OBT:000095
-name: greenhouse
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000097
-name: hospital environment
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000098
-name: household good
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000100
-name: industrial habitat
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000101
-name: intercellular
-synonym: "intercellularly" RELATED [TyDI:53082]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000102
-name: iron-rich environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000103
-name: laboratory equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000106
-name: liquid medium
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000108
-name: medical equipment
-synonym: "medical care equipment" RELATED [TyDI:53027]
-synonym: "medical care supply" RELATED [TyDI:53029]
-synonym: "medical device" RELATED [TyDI:53030]
-synonym: "medical supply" RELATED [TyDI:53028]
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000109
-name: medical product
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000110
-name: medical sample
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000111
-name: metaphyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000112
-name: microbial mat layer
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000113
-name: microflora
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000114
-name: microorganism
-synonym: "microbe" EXACT [TyDI:52385]
-synonym: "microbial" RELATED [TyDI:52386]
-is_a: OBT:000010 ! living organism
-
-[Term]
-id: OBT:000115
-name: microorganism part
-synonym: "microbe part" RELATED [TyDI:52345]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000119
-name: nest
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000121
-name: non-immune serum
-synonym: "nonimmune serum" EXACT [TyDI:52417]
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000124
-name: periphyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000140
-name: plant habitat
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000141
-name: polluted environment
-synonym: "contaminated site" RELATED [TyDI:52368]
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000145
-name: public equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000146
-name: rural area
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000149
-name: spore
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000151
-name: sterile water
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000155
-name: stromatolite
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000156
-name: subterrestrial habitat
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000158
-name: terrestrial habitat
-synonym: "terrestrial" RELATED [TyDI:53216]
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000160
-name: thermal area
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000161
-name: transport and storage equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000162
-name: transport equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000165
-name: urea solution
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000166
-name: volcanic area
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000167
-name: waste treatment environment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000168
-name: wet environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000170
-name: yeast extract
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000171
-name: zoo
-synonym: "zoo garden" RELATED [TyDI:55262]
-synonym: "zoo park" RELATED [TyDI:55261]
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000175
-name: abdomen
-synonym: "abdominal" RELATED [TyDI:55839]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000176
-name: acid environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000178
-name: adipocyte
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000180
-name: aerobic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000181
-name: aerobic environment
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000184
-name: agricultural pest
-is_a: OBT:000035 ! agricultural species
-
-[Term]
-id: OBT:000185
-name: agricultural tool
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000186
-name: air
-synonym: "atmospheric" EXACT [TyDI:53125]
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000187
-name: alkaline environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000190
-name: anaerobic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000191
-name: anaerobic environment
-synonym: "anoxic environments" EXACT [TyDI:55774]
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000193
-name: animal
-synonym: "animal host" RELATED [TyDI:54803]
-synonym: "animal species" RELATED [TyDI:54805]
-synonym: "animal-associated habitat" EXACT [TyDI:54804]
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000194
-name: animal farm
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000196
-name: animal tissue
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000197
-name: anoxic environment
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000198
-name: aquarium
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000199
-name: aquatic eukaryotic species
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000200
-name: arthropod part
-synonym: "arthropod organ" EXACT [TyDI:52938]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000201
-name: artificial water structure
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000202
-name: automated teller machine
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:000204
-name: back
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000205
-name: bandage
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000206
-name: banknote
-synonym: "bank note" EXACT [TyDI:56443]
-synonym: "currency note" EXACT [TyDI:56444]
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000208
-name: bathroom equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000209
-name: beak
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000210
-name: bedroom equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000212
-name: biofilm in natural environment
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000213
-name: biomat
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000214
-name: body
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000215
-name: body fluid
-synonym: "bodily fluid" EXACT [TyDI:55885]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000216
-name: body surface
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000217
-name: boot swab
-synonym: "overshoe" RELATED [TyDI:57230]
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000219
-name: carpet
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000220
-name: carpet tile
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000223
-name: catheter
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000224
-name: cattle-dipping vat
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000225
-name: cave
-is_a: OBT:000156 ! subterrestrial habitat
-
-[Term]
-id: OBT:000226
-name: ceiling tile
-is_a: OBT:003617 ! environmental surface
-
-[Term]
-id: OBT:000227
-name: cell sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000229
-name: cereal feed
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000231
-name: circulatory system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000232
-name: city
-synonym: "urban area" EXACT [TyDI:55802]
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000233
-name: cloud
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000234
-name: cloud water
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000237
-name: coelomic cavity
-synonym: "coelom" EXACT [TyDI:55848]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000238
-name: cold temperature environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000240
-name: commodity and primary derivative thereof
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000241
-name: composting reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000244
-name: contaminated site
-is_a: OBT:000141 ! polluted environment
-
-[Term]
-id: OBT:000246
-name: crop
-is_a: OBT:000034 ! agricultural product
-
-[Term]
-id: OBT:000247
-name: cruise ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000249
-name: cyanide treatment bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000250
-name: dairy farm equipment
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000253
-name: deep subsurface
-is_a: OBT:000156 ! subterrestrial habitat
-
-[Term]
-id: OBT:000254
-name: denitrification reactor
-synonym: "denitrifying reactor" EXACT [TyDI:55216]
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000255
-name: dental chair
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000256
-name: diagnostic equipment
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000258
-name: digestive system part
-synonym: "digestive tract part" EXACT [TyDI:54661]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000259
-name: ditch water
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000260
-name: domestic appliance
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000261
-name: drug
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000263
-name: dust
-synonym: "dust particle" EXACT [TyDI:54762]
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000264
-name: ear part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000266
-name: endolithic environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000267
-name: endosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000268
-name: enterocyte
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000269
-name: environment water
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000270
-name: exoskeleton
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000271
-name: exosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000272
-name: extra-genital
-synonym: "extragenital" EXACT [TyDI:54812]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000273
-name: extra-intestinal
-synonym: "extraintestinal" EXACT [TyDI:54796]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000274
-name: extracellular
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000277
-name: eye part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000280
-name: feeder cell
-is_a: OBT:000062 ! cell culture
-
-[Term]
-id: OBT:000281
-name: fertilizer
-is_a: OBT:000033 ! agricultural input
-
-[Term]
-id: OBT:000282
-name: finger
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000283
-name: fish pen
-synonym: "fish cage" EXACT [TyDI:55874]
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000284
-name: flagellum
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000285
-name: flesh
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000287
-name: forage
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000289
-name: freight transport equipment
-synonym: "good transport equipment" RELATED [TyDI:58103]
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000290
-name: fungi
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000291
-name: furniture
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000292
-name: garden
-is_a: OBT:000067 ! cultivated habitat
-
-[Term]
-id: OBT:000293
-name: geothermal area
-is_a: OBT:000160 ! thermal area
-
-[Term]
-id: OBT:000294
-name: germ cell
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000298
-name: granuloma
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000299
-name: grassland
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:000301
-name: hair
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000302
-name: haline environment
-synonym: "salty environment" RELATED [TyDI:55698]
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000303
-name: hatchery
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000306
-name: high osmolarity environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000307
-name: high pressure environment
-synonym: "high-pressure biotope" EXACT [TyDI:55693]
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000308
-name: high sulfur concentration environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000309
-name: high temperature environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000311
-name: horticulture farm
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000312
-name: hospital water
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000313
-name: host associated biofilm
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000314
-name: hotel equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000315
-name: house
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000316
-name: household product
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000318
-name: hydrotelluric environment
-synonym: "hydro-telluric" RELATED [TyDI:54758]
-synonym: "hydrotelluric" RELATED [TyDI:54759]
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000320
-name: immune cell
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000321
-name: immune system
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000322
-name: industrial chemical
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000323
-name: industrial product
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000324
-name: industrial site
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000325
-name: industrial water and effluent
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000326
-name: inland water body
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000327
-name: inside the body
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000328
-name: intensive care unit
-synonym: "ICU" EXACT [TyDI:54787]
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000329
-name: intracellular
-synonym: "intracellularly" RELATED [TyDI:50847]
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000330
-name: kitchen equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000331
-name: landfill
-is_a: OBT:000167 ! waste treatment environment
-
-[Term]
-id: OBT:000332
-name: lesion
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000333
-name: lower layer of a microbial mat
-is_a: OBT:000112 ! microbial mat layer
-
-[Term]
-id: OBT:000334
-name: lymphatic system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000336
-name: mariculture farm
-is_a: OBT:000045 ! aquaculture farm
-
-[Term]
-id: OBT:000337
-name: marine cage
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000338
-name: marine environment
-synonym: "marine" RELATED [TyDI:52984]
-synonym: "marine area" RELATED [TyDI:52987]
-synonym: "ocean" RELATED [TyDI:52986]
-synonym: "oceanic" RELATED [TyDI:52988]
-synonym: "sea" RELATED [TyDI:52985]
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000339
-name: meal
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000340
-name: meat and bone meal
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000341
-name: medical outfit
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000342
-name: medical sink
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000344
-name: mesosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000345
-name: metallic coin
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000346
-name: methanogenic reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000348
-name: microaerophilic environment
-synonym: "hypoxic environment" RELATED [TyDI:55783]
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000349
-name: microorganism gas vesicle
-is_a: OBT:000115 ! microorganism part
-
-[Term]
-id: OBT:000350
-name: mineral matter
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000351
-name: mire
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000352
-name: monument
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000354
-name: mushroom farm
-synonym: "mushroom factory" RELATED [TyDI:55316]
-synonym: "mushroom factory farm" EXACT [TyDI:55315]
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000355
-name: naval surface ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000356
-name: needle
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000357
-name: nervous system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000358
-name: neuston
-synonym: "neuston biofilm" EXACT [TyDI:54784]
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000360
-name: nutrient broth
-is_a: OBT:000106 ! liquid medium
-
-[Term]
-id: OBT:000362
-name: oomycete
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000363
-name: operating room
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000364
-name: organ
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000365
-name: organic matter
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000366
-name: oropharynx
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000373
-name: part of food
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000374
-name: pasture
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:000376
-name: perineum
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000377
-name: peritoneal cavity
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000388
-name: phyllosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000389
-name: phyllosphere part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000393
-name: plant
-synonym: "green plant" EXACT [TyDI:54809]
-synonym: "host plant" RELATED [TyDI:54808]
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000395
-name: plant part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000397
-name: prepared food
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000398
-name: prosthesis
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000400
-name: protozoa
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000403
-name: public building
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000404
-name: public toilet
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:000405
-name: public transport
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000406
-name: recreational fishing fish pond
-is_a: OBT:000093 ! fish pond
-
-[Term]
-id: OBT:000407
-name: respiratory tract
-synonym: "respiratory" RELATED [TyDI:55563]
-synonym: "respiratory airway" RELATED []
-synonym: "respiratory tree" RELATED [TyDI:55564]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000408
-name: respiratory tract part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000410
-name: rhizosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000411
-name: rhizosphere part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000412
-name: road part
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000413
-name: rodent nest
-is_a: OBT:000119 ! nest
-
-[Term]
-id: OBT:000414
-name: room
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000415
-name: room floor
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000416
-name: salivary sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000418
-name: ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000419
-name: ship hull
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000420
-name: shoe
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000421
-name: shower aerosol
-is_a: OBT:000030 ! aerosol
-
-[Term]
-id: OBT:000422
-name: shrimp culture pond
-synonym: "shrimp pond" EXACT [TyDI:54781]
-is_a: OBT:000046 ! aquaculture pond
-
-[Term]
-id: OBT:000423
-name: silo
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000424
-name: skin part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000425
-name: slough
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000426
-name: sludge blanket reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000427
-name: soil
-synonym: "soilborne" EXACT [TyDI:55680]
-is_a: OBT:000158 ! terrestrial habitat
-
-[Term]
-id: OBT:000428
-name: soil part
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000429
-name: solfatara
-synonym: "fumarole field" RELATED [TyDI:55674]
-synonym: "solfatara field" RELATED [TyDI:55673]
-is_a: OBT:000166 ! volcanic area
-
-[Term]
-id: OBT:000430
-name: spoiled food
-synonym: "contaminated food" RELATED [TyDI:50976]
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000431
-name: sputum sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000432
-name: starter culture
-synonym: "dry starter" RELATED [TyDI:52942]
-synonym: "starter" EXACT []
-is_a: OBT:000113 ! microflora
-
-[Term]
-id: OBT:000433
-name: sterile clean room
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000434
-name: storage equipment
-is_a: OBT:000161 ! transport and storage equipment
-created_by: claire
-creation_date: 2019-05-27T16:40:36Z
-
-[Term]
-id: OBT:000435
-name: stratosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000436
-name: subtropical area
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000437
-name: sulfide-rich environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000438
-name: surgical drain
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000442
-name: symbiosome
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000444
-name: syringe
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000445
-name: temperate zone
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000446
-name: terrestrial landscape
-is_a: OBT:000158 ! terrestrial habitat
-
-[Term]
-id: OBT:000447
-name: textile
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000448
-name: therapeutic equipment
-synonym: "therapy equipment" EXACT [TyDI:55458]
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000450
-name: thermophilic methanogenic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000451
-name: thermosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000455
-name: toilet equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000457
-name: traveller luggage
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000458
-name: tropical zone
-synonym: "tropical area" EXACT [TyDI:55365]
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000459
-name: troposphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000461
-name: ultrasound gel
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000462
-name: urine sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000463
-name: urogenital tract part
-synonym: "genitourinary system part" RELATED [TyDI:55857]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000464
-name: vaccine
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000465
-name: vertebrate part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000466
-name: wall
-synonym: "mural" RELATED [TyDI:56537]
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000467
-name: waste
-is_a: OBT:000167 ! waste treatment environment
-
-[Term]
-id: OBT:000468
-name: water
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000469
-name: water well
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000470
-name: Glomus vesiculiferum
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000471
-name: Intestinal mucosal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000474
-name: Saccharomyces cerevisiae starter
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000475
-name: abrasion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000476
-name: abscess
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000477
-name: additive
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000478
-name: agricultural waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000479
-name: air treatment unit
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000480
-name: airplane
-synonym: "aeroplane" RELATED [TyDI:55951]
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000481
-name: airport terminal
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000483
-name: alpine soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000484
-name: alveolar epithelium
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000485
-name: amniotic fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000486
-name: amoebas
-is_a: OBT:000400 ! protozoa
-
-[Term]
-id: OBT:000487
-name: anaerobic dechlorinating bioreactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000488
-name: anaerobic sludge blanket reactor
-synonym: "UASB reactor" EXACT []
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000489
-name: animal product and primary derivative thereof
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000490
-name: animal with age or sex property
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000491
-name: animal with disease
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000492
-name: antacid suspension
-is_a: OBT:000261 ! drug
-
-[Term]
-id: OBT:000493
-name: anthosphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000494
-name: anthosphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000495
-name: aqueous humour
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000496
-name: arthropod
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000497
-name: atherosclerotic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000498
-name: auricular prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000500
-name: bacteriocyte
-is_a: OBT:000178 ! adipocyte
-
-[Term]
-id: OBT:000501
-name: barley feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000502
-name: bathroom
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000503
-name: bathroom sink
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000504
-name: bathtub
-synonym: "bath tub" EXACT []
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000505
-name: bay
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000506
-name: bed as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000507
-name: bed sheet
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000508
-name: bedroom
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000509
-name: bedspread
-synonym: "bed cover" RELATED [TyDI:52109]
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000510
-name: beef farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000511
-name: beer yeast
-synonym: "brewer yeast" EXACT [TyDI:51000]
-synonym: "brewer's yeast" EXACT [TyDI:50998]
-synonym: "brewery yeast" EXACT [TyDI:51001]
-synonym: "brewing yeast" EXACT [TyDI:50999]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000514
-name: bile
-synonym: "gall" RELATED [TyDI:57924]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000515
-name: biliary tract
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000516
-name: biofertilizer
-is_a: OBT:000281 ! fertilizer
-
-[Term]
-id: OBT:000518
-name: bladder
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000519
-name: bladder stone
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000520
-name: blender
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000521
-name: blood
-synonym: "blood stream" RELATED [TyDI:58013]
-synonym: "bloodstream" RELATED [TyDI:58012]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000522
-name: blood meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000523
-name: blood plasma
-synonym: "plasma" RELATED [TyDI:57935]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000524
-name: blood serum
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000525
-name: blood vessel
-synonym: "vein" EXACT [TyDI:52363]
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000526
-name: bone fracture
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000527
-name: bone meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000528
-name: bone-anchored prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000529
-name: broncho-pulmonary segment
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000530
-name: bronchus
-synonym: "branchial" RELATED [TyDI:50479]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000531
-name: buffet
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000532
-name: building construction and demolition waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000533
-name: bulk soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000534
-name: bulk tank
-synonym: "bulk milk cooling tank" EXACT [TyDI:57148]
-synonym: "milk cooler" EXACT [TyDI:57149]
-is_a: OBT:000250 ! dairy farm equipment
-
-[Term]
-id: OBT:000535
-name: burn
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000536
-name: canker
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000537
-name: carcass
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000538
-name: caries
-synonym: "caries lesion" RELATED [TyDI:57836]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000539
-name: carpet floor
-is_a: OBT:000415 ! room floor
-
-[Term]
-id: OBT:000540
-name: carposphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000541
-name: carposphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000542
-name: carrier
-synonym: "vector" RELATED [TyDI:58258]
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000543
-name: catfish pond
-is_a: OBT:000406 ! recreational fishing fish pond
-
-[Term]
-id: OBT:000544
-name: caulosphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000545
-name: caulosphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000546
-name: cellar
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000547
-name: cellulose
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000548
-name: cellulosic substrate
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000549
-name: cereal flours feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000550
-name: cerebrospinal fluid
-synonym: "cerebro-spinal fluid" EXACT [TyDI:57962]
-synonym: "CSF" EXACT [TyDI:57960]
-synonym: "liquor cerebrospinalis" EXACT [TyDI:57961]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000551
-name: cervix
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000553
-name: chair
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000554
-name: chapel
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000556
-name: chest
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000557
-name: chyle
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000558
-name: chyme
-synonym: "chymus" EXACT [TyDI:57943]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000559
-name: circulatory system
-synonym: "cardiovascular system" EXACT [TyDI:57133]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000560
-name: clothe
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000561
-name: coal
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000562
-name: coast
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000564
-name: cochlear prosthesis
-synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:003645 ! ocular prosthesis
-
-[Term]
-id: OBT:000565
-name: coelom fluid
-synonym: "coelomic fluid" EXACT [TyDI:57793]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000566
-name: coffeemaker
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000567
-name: cold seep
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000568
-name: combustible liquid
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000569
-name: common millet feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000570
-name: composite food
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000571
-name: compost
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:000572
-name: conjunctiva
-is_a: OBT:000277 ! eye part
-
-[Term]
-id: OBT:000573
-name: cornea
-is_a: OBT:000277 ! eye part
-
-[Term]
-id: OBT:000574
-name: cosmetics
-is_a: OBT:000316 ! household product
-
-[Term]
-id: OBT:000575
-name: countertop
-synonym: "worktop" RELATED [TyDI:57193]
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000579
-name: culture system
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000580
-name: curtain
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000581
-name: cut
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000582
-name: cutting board
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000583
-name: dairy farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000584
-name: dairy starter culture
-synonym: "dairy starter" EXACT []
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000585
-name: dead matter
-synonym: "dead organic matter" RELATED [TyDI:50338]
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000586
-name: dead wood
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000587
-name: deep periodontal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000588
-name: deep sea
-synonym: "deep-sea" EXACT [TyDI:58017]
-synonym: "deep-sea environment" EXACT [TyDI:58016]
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000589
-name: deep tissue
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000590
-name: dental biofilm
-is_a: OBT:000313 ! host associated biofilm
-
-[Term]
-id: OBT:000591
-name: dental prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000592
-name: desert
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000593
-name: desert soil
-synonym: "desert" RELATED [TyDI:57776]
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000594
-name: dishcloth
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000595
-name: dishwasher
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000596
-name: domestic animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000597
-name: drinking water facility
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000601
-name: dune soil
-synonym: "dune" RELATED [TyDI:57158]
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000602
-name: ear
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000603
-name: ear canal
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000604
-name: ear wax
-synonym: "cerumen" EXACT [TyDI:57914]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000605
-name: earring hole
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000606
-name: earth
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000607
-name: eating and drinking place
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000608
-name: ectomycorrhizal fungus
-synonym: "ectomycorrhizal" RELATED [TyDI:57805]
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000610
-name: edible film
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000611
-name: effluent
-synonym: "industrial effluent" RELATED [TyDI:50516]
-is_a: OBT:000325 ! industrial water and effluent
-
-[Term]
-id: OBT:000612
-name: egg part
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000613
-name: embryonic structure
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000615
-name: endometrium
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000619
-name: epithelial layer
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000621
-name: excavation
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000622
-name: excreta
-synonym: "excretion" EXACT [TyDI:57919]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000623
-name: extra-uterus
-synonym: "extra-uterine" RELATED [TyDI:50542]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000624
-name: extractive industrial site
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000625
-name: extreme high temperature environment
-is_a: OBT:000309 ! high temperature environment
-
-[Term]
-id: OBT:000626
-name: extremely acid environment
-is_a: OBT:000176 ! acid environment
-
-[Term]
-id: OBT:000627
-name: eye
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000630
-name: fish farm
-is_a: OBT:000336 ! mariculture farm
-
-[Term]
-id: OBT:000631
-name: fish meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000633
-name: food for particular diet
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000634
-name: forest soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000636
-name: freezer
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000637
-name: freshwater aquarium
-is_a: OBT:000198 ! aquarium
-
-[Term]
-id: OBT:000638
-name: gall bladder
-synonym: "gallblader" EXACT [TyDI:57800]
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000639
-name: garden soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000640
-name: gastric acid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000641
-name: gastrointestinal tract
-synonym: "alimentary canal" RELATED [TyDI:54495]
-synonym: "digestive tract" RELATED [TyDI:54492]
-synonym: "gastrointestinal" RELATED [TyDI:54493]
-synonym: "GI tract" EXACT [TyDI:54491]
-synonym: "GIT" EXACT [TyDI:54494]
-synonym: "intestinal region" RELATED [TyDI:53836]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000642
-name: gastrointestinal tract part
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000643
-name: genital tract
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000644
-name: gill
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000645
-name: gingival crevice
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000646
-name: gingival lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000647
-name: glial cell
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000651
-name: granite stone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000653
-name: green forage
-is_a: OBT:000287 ! forage
-
-[Term]
-id: OBT:000654
-name: groin
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000655
-name: growing plant
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000658
-name: handkerchief
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000659
-name: harbor
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000660
-name: harvesting tool
-is_a: OBT:000185 ! agricultural tool
-
-[Term]
-id: OBT:000661
-name: head kidney
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000662
-name: heart valve
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000663
-name: hemodialysis machine
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000664
-name: hemolymph
-synonym: "haemolymph" EXACT [TyDI:56832]
-is_a: OBT:000200 ! arthropod part
-
-[Term]
-id: OBT:000666
-name: high chair tray
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000667
-name: high salt concentration environment
-is_a: OBT:000302 ! haline environment
-
-[Term]
-id: OBT:000668
-name: highly acid environment
-is_a: OBT:000176 ! acid environment
-
-[Term]
-id: OBT:000669
-name: home drainage system
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000670
-name: home food processing equipment
-synonym: "domestic food processing equipment" EXACT [TyDI:55574]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000671
-name: home heating system
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000672
-name: hospital gown
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000673
-name: hospital hot water
-is_a: OBT:000312 ! hospital water
-
-[Term]
-id: OBT:000674
-name: hot spring biomat
-is_a: OBT:000213 ! biomat
-
-[Term]
-id: OBT:000675
-name: hotel
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000676
-name: hotel carpet
-is_a: OBT:000219 ! carpet
-
-[Term]
-id: OBT:000677
-name: household waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000678
-name: human body
-is_a: OBT:000214 ! body
-
-[Term]
-id: OBT:000679
-name: humus
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000680
-name: humus soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000681
-name: ice
-is_a: OBT:000238 ! cold temperature environment
-
-[Term]
-id: OBT:000682
-name: indoor air
-is_a: OBT:000186 ! air
-
-[Term]
-id: OBT:000683
-name: industrial building
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000684
-name: industrial equipment
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000685
-name: industrial waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000686
-name: innate immune system
-is_a: OBT:000321 ! immune system
-
-[Term]
-id: OBT:000687
-name: inner ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000688
-name: insect part
-is_a: OBT:000200 ! arthropod part
-
-[Term]
-id: OBT:000689
-name: interstitial fluid
-synonym: "intercellular fluid" EXACT [TyDI:57238]
-synonym: "tissue fluid" EXACT [TyDI:57239]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000690
-name: intertidal zone
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000691
-name: intestinal content
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000692
-name: intra-uterus
-synonym: "intra-uterine" RELATED [TyDI:50499]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000693
-name: intravascular catheter
-is_a: OBT:000223 ! catheter
-
-[Term]
-id: OBT:000694
-name: invertebrate species
-synonym: "invertebrate" RELATED [TyDI:57989]
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000695
-name: jail
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000696
-name: jungle
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000697
-name: kitchen
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000698
-name: kitchen sink
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000699
-name: kitchen sponge
-synonym: "dish sponge" RELATED [TyDI:52187]
-synonym: "dish-washing sponge" RELATED [TyDI:52188]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000700
-name: laboratory animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000701
-name: laryngeal prosthetic device
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000702
-name: latrine
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000703
-name: leafy soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000704
-name: lentic water
-synonym: "stagnant water" RELATED [TyDI:50521]
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000705
-name: lentic water body
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:000706
-name: leukocyte
-synonym: "leucocyte" EXACT [TyDI:57142]
-synonym: "white blood cell" EXACT [TyDI:57143]
-is_a: OBT:000320 ! immune cell
-
-[Term]
-id: OBT:000707
-name: lichen
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000708
-name: light organ
-synonym: "light-emitting organ" EXACT [TyDI:50411]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000709
-name: limestone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000710
-name: lining
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000711
-name: liquid food
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000713
-name: lotic water body
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:000714
-name: lower respiratory tract
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000715
-name: lucerne
-is_a: OBT:000287 ! forage
-
-[Term]
-id: OBT:000716
-name: lung
-synonym: "pulmonary" RELATED [TyDI:54508]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000717
-name: lymph
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000718
-name: lymph node
-is_a: OBT:000334 ! lymphatic system part
-
-[Term]
-id: OBT:000719
-name: lymphatic system
-synonym: "lymphatic" RELATED [TyDI:50404]
-synonym: "lymphatics" EXACT [TyDI:50403]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000720
-name: maize feed
-synonym: "corn feed" NARROW []
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000721
-name: maize storage
-synonym: "corn storage" NARROW []
-is_a: OBT:000423 ! silo
-
-[Term]
-id: OBT:000722
-name: malt feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000723
-name: mammalian part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000724
-name: marine eukaryotic species
-is_a: OBT:000199 ! aquatic eukaryotic species
-
-[Term]
-id: OBT:000725
-name: marine freight transport equipment
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000726
-name: meat meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000727
-name: medical bed sheet
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000728
-name: medical glove
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000729
-name: medical mask
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000730
-name: animal membrane
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000731
-name: meninges
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000737
-name: microbial mat
-is_a: OBT:000213 ! biomat
-
-[Term]
-id: OBT:000738
-name: microwave oven
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000739
-name: mid-vaginal wall
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000740
-name: middle ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000741
-name: milking machine
-is_a: OBT:000250 ! dairy farm equipment
-
-[Term]
-id: OBT:000742
-name: mineral oil
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000743
-name: mineral soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000745
-name: moss
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000746
-name: mound
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000747
-name: mountain
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000748
-name: muddy water
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000749
-name: mural painting
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000750
-name: musculoskeletal system
-synonym: "locomotor apparatus" RELATED [TyDI:51092]
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000751
-name: musculoskeletal system part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000752
-name: mushroom
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000753
-name: mussel farm
-is_a: OBT:000336 ! mariculture farm
-
-[Term]
-id: OBT:000754
-name: nare
-synonym: "nostril" RELATED [TyDI:56380]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000755
-name: nasal cavity
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000756
-name: nasal epithelia
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000757
-name: nasopharynx
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000759
-name: natural gas
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000760
-name: necropolis
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000761
-name: necrotic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000765
-name: nerve
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000766
-name: nervous system
-synonym: "neurologic" EXACT [TyDI:57094]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000767
-name: nose
-synonym: "nasal" RELATED [TyDI:54437]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000768
-name: noxious plant
-is_a: OBT:000184 ! agricultural pest
-
-[Term]
-id: OBT:000773
-name: office
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000774
-name: oil tanker
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000775
-name: open-ocean
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000777
-name: organic waste
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000779
-name: ornithogenic soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000780
-name: osteolytic bone lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000781
-name: outdoor air
-is_a: OBT:000186 ! air
-
-[Term]
-id: OBT:000782
-name: outer ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000783
-name: ovary
-synonym: "ovaries" RELATED [TyDI:56007]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000786
-name: pacemaker
-is_a: OBT:003632 ! prosthetic cardiac device
-
-[Term]
-id: OBT:000787
-name: packaging
-is_a: OBT:000434 ! storage equipment
-
-[Term]
-id: OBT:000788
-name: packed lunch
-synonym: "bag lunch" RELATED [TyDI:58085]
-synonym: "box lunch" RELATED [TyDI:58087]
-synonym: "pack lunch" RELATED [TyDI:58088]
-synonym: "sack lunch" RELATED [TyDI:58086]
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000790
-name: pancreas
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000791
-name: pancreatic duct
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000792
-name: paper
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000793
-name: paper carton
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000794
-name: paper pulp
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000795
-name: passenger train
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000796
-name: perchlorate-contaminated site
-is_a: OBT:000244 ! contaminated site
-
-[Term]
-id: OBT:000797
-name: periodontal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000799
-name: peritoneal fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000800
-name: pest insect
-is_a: OBT:000184 ! agricultural pest
-
-[Term]
-id: OBT:000801
-name: phagocyte
-is_a: OBT:000320 ! immune cell
-
-[Term]
-id: OBT:000802
-name: pharyngeal mucosa
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000803
-name: phenol
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000806
-name: phylloplane
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000807
-name: phylloplane part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000808
-name: pig farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000810
-name: pillow as equipment
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000811
-name: placenta
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000812
-name: plant nodule
-is_a: OBT:000442 ! symbiosome
-
-[Term]
-id: OBT:000814
-name: plant organ
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000815
-name: plant product and primary derivative thereof
-synonym: "food processing plant" RELATED [TyDI:49608]
-synonym: "plant-derived foodstuff" RELATED [TyDI:56002]
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000816
-name: plant tissue
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000818
-name: pleural fluid
-synonym: "pleural effusion" RELATED [TyDI:57940]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000819
-name: pneumonic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000820
-name: porifera
-is_a: OBT:000199 ! aquatic eukaryotic species
-
-[Term]
-id: OBT:000823
-name: potluck
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000824
-name: poultry farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000825
-name: prepuce
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000826
-name: probe
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000828
-name: processed commodity and food
-is_a: OBT:000397 ! prepared food
-
-[Term]
-id: OBT:000829
-name: prostate
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000830
-name: prosthetic joint
-synonym: "joint prosthesis" EXACT []
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000831
-name: pus
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000832
-name: quinoa feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000833
-name: rash
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000834
-name: raw primary commodities
-synonym: "raw food" RELATED [TyDI:57190]
-synonym: "uncooked food" RELATED [TyDI:57189]
-synonym: "unprocessed food" RELATED [TyDI:57187]
-synonym: "untreated food" RELATED [TyDI:57188]
-is_a: OBT:000397 ! prepared food
-
-[Term]
-id: OBT:000835
-name: ready made meal
-synonym: "prepackaged meal" RELATED [TyDI:58097]
-synonym: "ready meal" RELATED [TyDI:58098]
-synonym: "ready to eat meal" RELATED [TyDI:58100]
-synonym: "TV dinner" RELATED [TyDI:58099]
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000836
-name: reef surface biofilm
-is_a: OBT:000212 ! biofilm in natural environment
-
-[Term]
-id: OBT:000837
-name: refrigerator
-synonym: "fridge" RELATED [TyDI:57118]
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000838
-name: research and study center
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000839
-name: residential carpet
-is_a: OBT:000219 ! carpet
-
-[Term]
-id: OBT:000840
-name: residential toilet
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000841
-name: respiratory therapy equipment
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000842
-name: rice feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000843
-name: road
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000844
-name: road junction
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000845
-name: road side
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000846
-name: rock
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000847
-name: rock scraping
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000849
-name: root part
-is_a: OBT:000411 ! rhizosphere part
-
-[Term]
-id: OBT:000851
-name: rye feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000852
-name: salt crust
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000853
-name: sandstone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000854
-name: sandstone monument
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000855
-name: sandy soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000856
-name: sauna
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000857
-name: savannah
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000858
-name: school
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000859
-name: school bus
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000860
-name: scratch
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000861
-name: scrub as clothing
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000862
-name: seabed
-synonym: "sea floor" EXACT [TyDI:54745]
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000863
-name: secretion
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000864
-name: sensor
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000866
-name: ship ballast
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000867
-name: ship ballast water
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000868
-name: ship tank
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000869
-name: shower
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000870
-name: shrimp hatchery
-is_a: OBT:000303 ! hatchery
-
-[Term]
-id: OBT:000871
-name: silage
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000873
-name: sink drain
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000874
-name: site contaminated with organic compound
-is_a: OBT:000244 ! contaminated site
-
-[Term]
-id: OBT:000875
-name: skin
-synonym: "cutaneous" RELATED [TyDI:54464]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000876
-name: skin bump
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000877
-name: skin nodule
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000878
-name: skin papule
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000881
-name: snow
-is_a: OBT:000238 ! cold temperature environment
-
-[Term]
-id: OBT:000882
-name: sofa as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000883
-name: soft tissue
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000884
-name: soil crust
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000885
-name: soil matter
-is_a: OBT:000428 ! soil part
-
-[Term]
-id: OBT:000886
-name: sorghum feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000887
-name: spinal cord
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000889
-name: spirometer
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000890
-name: spleen
-synonym: "splenic" EXACT [TyDI:51044]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000894
-name: starter yeast
-synonym: "commercial starter" EXACT [TyDI:50918]
-synonym: "commercial yeast" EXACT [TyDI:50920]
-synonym: "yeast starter" EXACT [TyDI:50919]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000895
-name: stomach content
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000896
-name: stool as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000898
-name: subgingival biofilm
-is_a: OBT:000313 ! host associated biofilm
-
-[Term]
-id: OBT:000899
-name: subway
-synonym: "metro" RELATED [TyDI:56961]
-synonym: "metropolitan" RELATED [TyDI:56960]
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000900
-name: sulfide-oxidizing bioreactor
-is_a: OBT:000180 ! aerobic bioreactor
-
-[Term]
-id: OBT:000901
-name: sulfidogenic bioreactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000902
-name: surface of food
-is_a: OBT:000373 ! part of food
-
-[Term]
-id: OBT:000903
-name: surface soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000904
-name: surface water
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000905
-name: surgical cap
-synonym: "scrub cap" RELATED [TyDI:57233]
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000907
-name: synovial fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000908
-name: table as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000909
-name: tableware
-synonym: "dishware" RELATED [TyDI:57196]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000910
-name: tap
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000911
-name: terminal airway
-synonym: "airway" RELATED [TyDI:57983]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000912
-name: terrestrial plant
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000913
-name: testis
-synonym: "testes" EXACT [TyDI:57109]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000915
-name: therapeutic ultrasound equipment
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000916
-name: thermometer as medical device
-synonym: "<new synonym>" RELATED [TyDI:57022]
-synonym: "clinical thermometer" RELATED [TyDI:57023]
-synonym: "hospital thermometer" RELATED [TyDI:57024]
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000917
-name: thermophilic anaerobic methanogenic reactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000918
-name: throat
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000919
-name: throat swab
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000920
-name: toilet
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000921
-name: toilet bowl
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000922
-name: toilet seat
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000923
-name: toiletries
-is_a: OBT:000316 ! household product
-
-[Term]
-id: OBT:000924
-name: tomb
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000925
-name: toundra
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000926
-name: towel
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000927
-name: tree part
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000929
-name: trona crust
-synonym: "kaum crust" EXACT [TyDI:56987]
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000930
-name: tropical country
-is_a: OBT:000458 ! tropical zone
-
-[Term]
-id: OBT:000931
-name: trypanosome
-is_a: OBT:000400 ! protozoa
-
-[Term]
-id: OBT:000932
-name: tuberculoid granuloma
-is_a: OBT:000298 ! granuloma
-
-[Term]
-id: OBT:000933
-name: ulcer
-synonym: "ulceration" RELATED [TyDI:50416]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000934
-name: ulcerative lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000935
-name: upland
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000936
-name: upper respiratory tract
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000937
-name: ureter
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000938
-name: urethra
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000939
-name: urinary catheter
-is_a: OBT:000223 ! catheter
-
-[Term]
-id: OBT:000940
-name: urinary tract
-synonym: "urinary" RELATED [TyDI:50526]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000941
-name: urogenital tract
-synonym: "urogenital" RELATED [TyDI:56017]
-synonym: "urogenital area" RELATED [TyDI:56018]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000942
-name: uterus
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000943
-name: vagina
-synonym: "vaginal" RELATED [TyDI:50358]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000944
-name: valley
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000945
-name: vascular
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000946
-name: vertebrate
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000947
-name: veterinary drug
-is_a: OBT:003680 ! veterinary product
-
-[Term]
-id: OBT:000948
-name: vitreous fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000949
-name: vitreous humor
-synonym: "vitreous body" EXACT [TyDI:57966]
-synonym: "vitreous humour" EXACT [TyDI:57965]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000950
-name: volcanic soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000951
-name: volcano
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000952
-name: vomit
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000953
-name: washbasin
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000954
-name: washing machine
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000955
-name: water cooling system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000956
-name: water droplet
-is_a: OBT:000468 ! water
-
-[Term]
-id: OBT:000957
-name: water from air and water system
-is_a: OBT:000325 ! industrial water and effluent
-
-[Term]
-id: OBT:000958
-name: water heater system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000959
-name: water storage system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000960
-name: water transport structure
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000961
-name: water treatment plant
-synonym: "water treatment facility" RELATED [TyDI:54688]
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000962
-name: water vapor
-is_a: OBT:000468 ! water
-
-[Term]
-id: OBT:000963
-name: welfare center
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000964
-name: wetland
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000965
-name: wheat feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000966
-name: whirlpool bath
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000967
-name: wild animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000968
-name: wine yeast
-synonym: "oenological yeast" EXACT [TyDI:50875]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000969
-name: woody landscape
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000970
-name: wound
-synonym: "injury" EXACT [TyDI:50484]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000971
-name: zoo animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000972
-name: Asteraceae
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:000973
-name: Cerrado
-is_a: OBT:000857 ! savannah
-
-[Term]
-id: OBT:000974
-name: Crassulaceae
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:000975
-name: PCE contaminated site
-synonym: "perchloroethylene contaminated site" EXACT [TyDI:50826]
-synonym: "tetrachloroethene contaminated site" EXACT [TyDI:50825]
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:000976
-name: Tasmanian devil
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:000977
-name: abalone
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:000978
-name: agranulocyte
-is_a: OBT:000706 ! leukocyte
-
-[Term]
-id: OBT:000979
-name: air conditioning system
-synonym: "air conditioner" EXACT [TyDI:53043]
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:000980
-name: air filter
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:000981
-name: ale yeast
-synonym: "ale brewer's yeast" EXACT [TyDI:50884]
-is_a: OBT:000511 ! beer yeast
-
-[Term]
-id: OBT:000982
-name: alfalfa silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:000983
-name: alkaline salt crust
-is_a: OBT:000852 ! salt crust
-
-[Term]
-id: OBT:000984
-name: animal based juice
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:000985
-name: animal waste
-is_a: OBT:000777 ! organic waste
-
-[Term]
-id: OBT:000986
-name: animal with life stage property
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:000987
-name: annelid
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:000988
-name: anus
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:000989
-name: arachnid
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:000990
-name: artery
-is_a: OBT:000525 ! blood vessel
-
-[Term]
-id: OBT:000991
-name: artic valley
-is_a: OBT:000944 ! valley
-
-[Term]
-id: OBT:000992
-name: ascidian
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:000993
-name: ash dump
-synonym: "ash dump site" EXACT [TyDI:50465]
-synonym: "ash dumping site" EXACT [TyDI:50466]
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:000994
-name: baby diaper
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:000995
-name: baby wipe
-synonym: "moist towel" RELATED [TyDI:56846]
-synonym: "wet towel" RELATED [TyDI:56847]
-synonym: "wet wipe" RELATED [TyDI:56848]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:000996
-name: backswamp
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:000997
-name: backwater
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:000998
-name: bacteriome
-is_a: OBT:000688 ! insect part
-
-[Term]
-id: OBT:000999
-name: baking powder
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001000
-name: baking soda
-synonym: "sodium bicarbonate" EXACT [TyDI:50899]
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001001
-name: bamboo
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001002
-name: bark
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001003
-name: barrier flat
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001004
-name: benzene-contaminated site
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:001006
-name: bird and reptile GIT part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001009
-name: bog
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001010
-name: boiler
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001011
-name: bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001012
-name: bone caries
-is_a: OBT:000538 ! caries
-
-[Term]
-id: OBT:001013
-name: botanical garden soil
-is_a: OBT:000639 ! garden soil
-
-[Term]
-id: OBT:001014
-name: brain abcess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001015
-name: branch
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001016
-name: brasserie
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001017
-name: breast
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001018
-name: breast milk
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001020
-name: buccal
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001021
-name: bulbous plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001022
-name: cafeteria
-synonym: "canteen" RELATED [TyDI:58190]
-synonym: "dining hall" RELATED [TyDI:58191]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001023
-name: café
-synonym: "coffee shop" RELATED [TyDI:58107]
-synonym: "coffeehouse" RELATED [TyDI:58106]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001024
-name: calcereous rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001025
-name: calorifier
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001026
-name: canopy humus
-is_a: OBT:000679 ! humus
-
-[Term]
-id: OBT:001027
-name: cargo oil tank
-is_a: OBT:000868 ! ship tank
-
-[Term]
-id: OBT:001028
-name: central nervous system
-is_a: OBT:000766 ! nervous system
-
-[Term]
-id: OBT:001029
-name: cereal and pseudo-cereal dough-based product
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001030
-name: cheese starter culture
-is_a: OBT:000584 ! dairy starter culture
-
-[Term]
-id: OBT:001031
-name: chemical plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001032
-name: chewing stick
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001033
-name: chipboard factory
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001034
-name: chlorine-contaminated site
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:001036
-name: chocolate product
-synonym: "chocolate" RELATED [TyDI:50114]
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001037
-name: clay
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001038
-name: clean room
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001039
-name: coal spoil
-synonym: "coal residue" RELATED [TyDI:49847]
-is_a: OBT:000561 ! coal
-
-[Term]
-id: OBT:001040
-name: coastal fish farm
-is_a: OBT:000630 ! fish farm
-
-[Term]
-id: OBT:001041
-name: coastal wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001042
-name: college
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001044
-name: condiment
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001045
-name: confectionery
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001046
-name: cooling tower
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001047
-name: cooling water
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001048
-name: coral
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001049
-name: corneal ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001050
-name: cortex
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001051
-name: cortical bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001052
-name: cotton swab
-synonym: "cotton bud" RELATED [TyDI:56786]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001053
-name: cotton-waste compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001055
-name: creek
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001056
-name: creosol
-is_a: OBT:000803 ! phenol
-
-[Term]
-id: OBT:001057
-name: crucifer
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001058
-name: crude oil
-synonym: "fossil fuel" RELATED [TyDI:55651]
-synonym: "petroleum" EXACT [TyDI:55652]
-is_a: OBT:000742 ! mineral oil
-
-[Term]
-id: OBT:001059
-name: crustacean
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:001060
-name: cuticle
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001061
-name: cyanobacterial mat
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:001062
-name: dairy farming waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001063
-name: dead organism
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001064
-name: dead tissue
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001065
-name: decaying matter
-synonym: "decaying organic matter" RELATED [TyDI:51801]
-synonym: "saprophyte" RELATED [TyDI:51800]
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001066
-name: defrosted food
-synonym: " thawed food" EXACT [TyDI:55720]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001067
-name: dental abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001068
-name: dental caries
-synonym: "dental cavity" EXACT [TyDI:49761]
-synonym: "tooth decay" RELATED [TyDI:49760]
-is_a: OBT:000538 ! caries
-
-[Term]
-id: OBT:001069
-name: desert rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001070
-name: dietary supplement
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001071
-name: dining car
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001072
-name: dinner plate
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001073
-name: dish
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001074
-name: district heating plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001075
-name: drainage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001076
-name: drainage canal
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001077
-name: drainage ditch
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001078
-name: drink
-synonym: "beverage" EXACT [TyDI:50020]
-is_a: OBT:000711 ! liquid food
-
-[Term]
-id: OBT:001079
-name: drinking glass
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001080
-name: drinking water filter
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001081
-name: drinking water reservoir
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001082
-name: drinking water supply
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001083
-name: ear thermometer
-synonym: "tympanic thermometer" RELATED [TyDI:56942]
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001084
-name: eating utensil
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001085
-name: eel farm
-is_a: OBT:000630 ! fish farm
-
-[Term]
-id: OBT:001086
-name: egg and egg product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001087
-name: empyema
-is_a: OBT:000831 ! pus
-
-[Term]
-id: OBT:001088
-name: endodermis
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001089
-name: epidermis
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001090
-name: epidermis part
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001091
-name: epithelium
-synonym: "epithelial" RELATED [TyDI:49861]
-is_a: OBT:000619 ! epithelial layer
-
-[Term]
-id: OBT:001092
-name: estuary
-is_a: OBT:000690 ! intertidal zone
-
-[Term]
-id: OBT:001093
-name: evaporator
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001094
-name: extractive industry equipment
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001096
-name: facial tissue
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001097
-name: factory
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001099
-name: fast food restaurant
-synonym: " quick service restaurant" RELATED [TyDI:58177]
-synonym: "fast-food restaurant" RELATED [TyDI:58176]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001100
-name: fat body
-is_a: OBT:000688 ! insect part
-
-[Term]
-id: OBT:001101
-name: feather pillow
-is_a: OBT:000810 ! pillow as equipment
-
-[Term]
-id: OBT:001102
-name: feces
-synonym: "dropping" RELATED [TyDI:52876]
-synonym: "dung" EXACT [TyDI:52875]
-synonym: "faecal" RELATED [TyDI:52880]
-synonym: "faeces" EXACT [TyDI:52874]
-synonym: "frass" RELATED [TyDI:52879]
-synonym: "pellet" RELATED [TyDI:52877]
-synonym: "stool" RELATED [TyDI:52878]
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001103
-name: female animal
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:001104
-name: fen
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001106
-name: flower part
-is_a: OBT:000494 ! anthosphere part
-
-[Term]
-id: OBT:001108
-name: food booth
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001109
-name: food cart
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001110
-name: food container
-synonym: "food package" RELATED []
-synonym: "food wrapping" RELATED []
-is_a: OBT:000787 ! packaging
-
-[Term]
-id: OBT:001111
-name: food flavour
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001112
-name: food processing appliance
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001113
-name: food processing effluent
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001114
-name: food rind
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001115
-name: food truck
-synonym: "food-vending vehicle" RELATED [TyDI:58180]
-synonym: "lunch truck" RELATED [TyDI:58181]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001116
-name: foot
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001117
-name: foregut
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001118
-name: forehead thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001119
-name: forest
-is_a: OBT:000969 ! woody landscape
-
-[Term]
-id: OBT:001120
-name: forest humus
-is_a: OBT:000679 ! humus
-
-[Term]
-id: OBT:001121
-name: freshwater wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001122
-name: fruit and primary derivative thereof
-synonym: "fruit" RELATED [TyDI:51591]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001123
-name: fruit part
-is_a: OBT:000541 ! carposphere part
-
-[Term]
-id: OBT:001124
-name: furuncle fluid
-is_a: OBT:000831 ! pus
-
-[Term]
-id: OBT:001125
-name: garden plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001126
-name: garden vegetable and primary derivative thereof
-synonym: "vegetable" RELATED [TyDI:51704]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001127
-name: gas seep
-is_a: OBT:000759 ! natural gas
-
-[Term]
-id: OBT:001128
-name: gastric antrum
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001129
-name: gastric body
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001130
-name: gelatine as ingredient
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001132
-name: grain and primary derivative thereof
-synonym: "oilseed" RELATED [TyDI:51242]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001133
-name: granitic rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001134
-name: granulocyte
-is_a: OBT:000706 ! leukocyte
-
-[Term]
-id: OBT:001135
-name: grass plant
-synonym: "grass" EXACT [TyDI:49773]
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001136
-name: grass silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001138
-name: ground food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001139
-name: guar gum
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001140
-name: gut
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001141
-name: hairspray
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001142
-name: head
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001143
-name: hindgut
-synonym: "hind-gut" RELATED [TyDI:50111]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001144
-name: hip bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001145
-name: home-made food
-synonym: "home-prepared food" RELATED [TyDI:51032]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001146
-name: honey and apiculture product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001147
-name: hoof
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001148
-name: horticultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001149
-name: hot water tank
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001150
-name: hotel bathroom
-is_a: OBT:000502 ! bathroom
-
-[Term]
-id: OBT:001151
-name: human Bartholin abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001152
-name: human appendix abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001153
-name: humidifier
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:001154
-name: hypersaline microbial mat
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:001155
-name: incontinence pad
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001157
-name: industrial organic waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001158
-name: industrial scrap
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001159
-name: industrial sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001160
-name: indwelling urinary catheter
-is_a: OBT:000939 ! urinary catheter
-
-[Term]
-id: OBT:001161
-name: infant formula
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001162
-name: ingredient for hot drink
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001163
-name: insect
-synonym: "insect host" RELATED [TyDI:51900]
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:001164
-name: irrigation ditch
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001165
-name: jellyfish
-synonym: "sea jelly" RELATED [TyDI:52321]
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001166
-name: joint
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001167
-name: kerosene
-is_a: OBT:000568 ! combustible liquid
-
-[Term]
-id: OBT:001168
-name: kitchen garbage
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001169
-name: laboratory
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001170
-name: lager yeast
-synonym: "lager brewer's yeast" EXACT [TyDI:50892]
-synonym: "lager-brewing yeast" EXACT [TyDI:50891]
-is_a: OBT:000511 ! beer yeast
-
-[Term]
-id: OBT:001171
-name: lake
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:001172
-name: landfill site waste
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001173
-name: leachate
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001174
-name: leaf
-synonym: "plant leaf" EXACT [TyDI:51761]
-is_a: OBT:000807 ! phylloplane part
-
-[Term]
-id: OBT:001175
-name: leaf part
-is_a: OBT:000807 ! phylloplane part
-
-[Term]
-id: OBT:001176
-name: leg
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001177
-name: legume seed and primary derivative thereof
-synonym: "legume" RELATED [TyDI:50093]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001178
-name: lenticel
-is_a: OBT:000545 ! caulosphere part
-
-[Term]
-id: OBT:001179
-name: leopard
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001180
-name: lignocellulose
-is_a: OBT:000547 ! cellulose
-
-[Term]
-id: OBT:001181
-name: liquid agricultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001182
-name: liver abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001183
-name: livestock habitat
-is_a: OBT:000003 ! animal habitat
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:001184
-name: lower gastrointestinal tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001185
-name: lumber
-is_a: OBT:000586 ! dead wood
-
-[Term]
-id: OBT:001186
-name: lunch box
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001187
-name: lynx
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001188
-name: lyophilized milk starter
-is_a: OBT:000584 ! dairy starter culture
-
-[Term]
-id: OBT:001189
-name: machinery
-synonym: "machine" RELATED [TyDI:49876]
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001190
-name: maize silage
-synonym: "corn silage" NARROW []
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001191
-name: malachite green effluent
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001192
-name: male animal
-synonym: "male" EXACT [TyDI:49873]
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:001193
-name: mammary gland
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001194
-name: manure compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001195
-name: marine coast
-synonym: "coastal marine environment" EXACT [TyDI:49836]
-is_a: OBT:000562 ! coast
-
-[Term]
-id: OBT:001196
-name: marine rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001198
-name: marsh
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001199
-name: mashed food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001200
-name: meat and meat product
-synonym: "animal meat" EXACT [TyDI:52959]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001201
-name: meristem
-synonym: "meristemic" RELATED [TyDI:49807]
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001202
-name: mesentery
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001206
-name: midge
-is_a: OBT:000800 ! pest insect
-
-[Term]
-id: OBT:001207
-name: midgut
-synonym: "embryonic digestive tube" RELATED [TyDI:55725]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001208
-name: milk and milk product
-synonym: "dairy product" RELATED [TyDI:49802]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001209
-name: milled food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001210
-name: mine
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001211
-name: mine drainage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001212
-name: mine waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001213
-name: model plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001215
-name: mollusc
-synonym: "mollusca" RELATED [TyDI:55717]
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001216
-name: moor
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001217
-name: mouth part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001218
-name: mucosal tissue
-synonym: "mucosa" RELATED [TyDI:51869]
-is_a: OBT:000710 ! lining
-
-[Term]
-id: OBT:001219
-name: mucous membrane
-synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001220
-name: mucus
-synonym: "mucous" RELATED [TyDI:49731]
-synonym: "mucous flow" RELATED [TyDI:49730]
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001221
-name: mud
-synonym: "ooze" RELATED [TyDI:51894]
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001222
-name: mud volcano
-is_a: OBT:000951 ! volcano
-
-[Term]
-id: OBT:001223
-name: mudpit
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001224
-name: municipal sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001225
-name: municipal solid waste
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001226
-name: muscle
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001227
-name: nasal passage abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001228
-name: nasal secretion
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001229
-name: neck
-synonym: "cervical" RELATED [TyDI:50053]
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001230
-name: nematode
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001231
-name: nursing home
-is_a: OBT:000963 ! welfare center
-
-[Term]
-id: OBT:001232
-name: nut and primary derivative thereof
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001234
-name: offal and product thereof
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001235
-name: oil field
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001236
-name: oil industry
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001237
-name: oil well
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001238
-name: oilfruit and primary derivative thereof
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001239
-name: oral thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001241
-name: oven
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001242
-name: panda
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001243
-name: panty liner
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001244
-name: paper gown
-is_a: OBT:000672 ! hospital gown
-
-[Term]
-id: OBT:001245
-name: paper towel
-synonym: "kitchen roll" RELATED [TyDI:52262]
-is_a: OBT:000926 ! towel
-
-[Term]
-id: OBT:001246
-name: parenchyma
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001247
-name: pea family
-synonym: "Fabaceace" EXACT [TyDI:50092]
-synonym: "legume" RELATED [TyDI:50093]
-synonym: "Leguminosae" RELATED [TyDI:50090]
-synonym: "leguminous plant" RELATED [TyDI:50091]
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001248
-name: peptic ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001249
-name: perineal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001250
-name: periodontal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001251
-name: peripheral nervous system
-synonym: "PNS" EXACT [TyDI:53169]
-is_a: OBT:000766 ! nervous system
-
-[Term]
-id: OBT:001252
-name: perirectal area
-synonym: "perianal area" EXACT [TyDI:56377]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001253
-name: peritoneum
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001254
-name: pet
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:001256
-name: piping system
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001257
-name: plankton
-synonym: "planktonic" EXACT [TyDI:49767]
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001258
-name: plant material
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001259
-name: plantlet
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001260
-name: pond
-synonym: "freshwater pond" RELATED [TyDI:51936]
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:001261
-name: pond water
-synonym: "pond" RELATED [TyDI:51935]
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001262
-name: posterior intestinal content
-is_a: OBT:000691 ! intestinal content
-
-[Term]
-id: OBT:001263
-name: potato silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001264
-name: power plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001265
-name: prepared meat
-synonym: "processed meat" EXACT [TyDI:51401]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001266
-name: preserved food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001267
-name: pressed food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001268
-name: primate part
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001269
-name: probiotic food
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001270
-name: public house
-synonym: "tavern" RELATED [TyDI:58118]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001271
-name: public toilet seat
-is_a: OBT:000922 ! toilet seat
-
-[Term]
-id: OBT:001273
-name: quarry
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001274
-name: rainwater tank
-synonym: "water butt" RELATED [TyDI:58044]
-is_a: OBT:000959 ! water storage system
-
-[Term]
-id: OBT:001275
-name: raw meat
-synonym: "undercooked meat" RELATED [TyDI:51753]
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001276
-name: raw milk
-synonym: "unpasteurized milk" EXACT [TyDI:49881]
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001277
-name: raw seafood
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001278
-name: ready-to-eat meal
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001279
-name: rectal thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001281
-name: refinery
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001282
-name: reptile
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:001283
-name: restaurant
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001284
-name: rice silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001285
-name: river
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001286
-name: root cap
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:001287
-name: root cortex part
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:001289
-name: ruminant digestive system part
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001290
-name: saline wetland
-synonym: "saline-wetland" EXACT [TyDI:52885]
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001291
-name: saliva
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001292
-name: salt-tolerant plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001293
-name: sand
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001294
-name: sandy beach
-is_a: OBT:000855 ! sandy soil
-
-[Term]
-id: OBT:001295
-name: sandy bulk soil
-is_a: OBT:000533 ! bulk soil
-
-[Term]
-id: OBT:001296
-name: sanitary towel
-synonym: "menstrual pad" RELATED [TyDI:56761]
-synonym: "sanitary napkin" RELATED [TyDI:56762]
-synonym: "sanitary pad" RELATED [TyDI:56763]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001297
-name: sap
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001298
-name: sawmill
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001299
-name: sclerenchyma
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001300
-name: sea ice
-is_a: OBT:000681 ! ice
-
-[Term]
-id: OBT:001301
-name: seafood and seafood product
-synonym: "fresh water food" RELATED [TyDI:51756]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001302
-name: sebum
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001303
-name: sediment
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001304
-name: seedling
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001305
-name: self-heated organic material
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001306
-name: semen
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001307
-name: sewage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001308
-name: sewage oxidation pond
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001309
-name: sewage sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001310
-name: shale sandstone
-is_a: OBT:000853 ! sandstone
-
-[Term]
-id: OBT:001311
-name: shampoo
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001312
-name: shaving cream
-synonym: "shaving foam" RELATED [TyDI:56839]
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001313
-name: ship scrapping waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001314
-name: shore
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001315
-name: shoreline
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001316
-name: silcone rubber voice prothesis
-is_a: OBT:000701 ! laryngeal prosthetic device
-
-[Term]
-id: OBT:001317
-name: silt
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001319
-name: skeleton
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001320
-name: skin ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001321
-name: slaughtering product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001322
-name: slaugterhouse equipment
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001323
-name: snack
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001324
-name: soap
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001325
-name: soft tissue abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001326
-name: solfataric soil
-is_a: OBT:000950 ! volcanic soil
-
-[Term]
-id: OBT:001327
-name: solid agricultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001328
-name: soup
-is_a: OBT:000711 ! liquid food
-
-[Term]
-id: OBT:001331
-name: splenic abcess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001332
-name: sponge
-is_a: OBT:000820 ! porifera
-
-[Term]
-id: OBT:001333
-name: spring
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001334
-name: sprout
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001335
-name: sputum
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001336
-name: stem part
-is_a: OBT:000545 ! caulosphere part
-
-[Term]
-id: OBT:001337
-name: stew
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001338
-name: stratified water
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001339
-name: subcutaneous abscess-like lesion
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001340
-name: sugar
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001341
-name: surface of cheese
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001342
-name: surface smear
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001343
-name: surgical gown
-is_a: OBT:000672 ! hospital gown
-
-[Term]
-id: OBT:001344
-name: swamp
-synonym: "swamp forest" EXACT [TyDI:49819]
-synonym: "wooded swamp" EXACT [TyDI:49818]
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001345
-name: sweat
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001346
-name: tail
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001347
-name: take-away restaurant
-synonym: "take away restaurant" RELATED [TyDI:58194]
-synonym: "takeaway shop" RELATED [TyDI:58195]
-synonym: "takeout restaurant" RELATED [TyDI:58196]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001348
-name: tampon
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001349
-name: tank water
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001350
-name: tears
-synonym: "tear" EXACT [TyDI:49813]
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001351
-name: teat
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001352
-name: teat canal
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001353
-name: temperature sensor
-synonym: "temperature probe" RELATED [TyDI:51770]
-is_a: OBT:000864 ! sensor
-
-[Term]
-id: OBT:001354
-name: terrestial wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001355
-name: tidal creek
-is_a: OBT:000690 ! intertidal zone
-
-[Term]
-id: OBT:001356
-name: toothbrush
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001357
-name: toothpaste
-synonym: "dentifrice" RELATED [TyDI:56853]
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001358
-name: trachea
-is_a: OBT:000529 ! broncho-pulmonary segment
-
-[Term]
-id: OBT:001359
-name: treated wood
-is_a: OBT:000586 ! dead wood
-is_a: OBT:003742 ! wood waste
-
-[Term]
-id: OBT:001360
-name: tree
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001361
-name: trunk
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001362
-name: tuber
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001363
-name: twig
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001364
-name: udder parenchyma
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001365
-name: university
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001366
-name: upper gastrointestinal tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001367
-name: urine
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001368
-name: vaginal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001369
-name: vaginal secretion
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001370
-name: vascular tissue
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001371
-name: vegetable garden soil
-is_a: OBT:000639 ! garden soil
-
-[Term]
-id: OBT:001373
-name: warehouse
-synonym: "storehouse" RELATED [TyDI:51804]
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001374
-name: warm-blooded animal
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:001375
-name: waste food compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001376
-name: water canal
-synonym: "canal" EXACT [TyDI:51944]
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001377
-name: water column
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001378
-name: water heater
-synonym: "hot water system " RELATED [TyDI:57043]
-synonym: "storage water heater" RELATED [TyDI:57044]
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001379
-name: water of an humidifier
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001380
-name: water system
-synonym: "water supply" RELATED [TyDI:51773]
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001381
-name: water tank
-synonym: "water storage tank" EXACT [TyDI:53205]
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001383
-name: wood
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001384
-name: working animal
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:001385
-name: worm
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001387
-name: yolk sac
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001388
-name: Achillea millefolium
-is_a: OBT:000972 ! Asteraceae
-
-[Term]
-id: OBT:001389
-name: Allium
-is_a: OBT:001021 ! bulbous plant
-
-[Term]
-id: OBT:001390
-name: Arabidopsis
-is_a: OBT:001213 ! model plant
-
-[Term]
-id: OBT:001391
-name: Brassica
-is_a: OBT:001057 ! crucifer
-
-[Term]
-id: OBT:001392
-name: Osmitopsis asteriscoides
-is_a: OBT:000972 ! Asteraceae
-
-[Term]
-id: OBT:001393
-name: Salicornioideae
-is_a: OBT:001292 ! salt-tolerant plant
-
-[Term]
-id: OBT:001394
-name: abomasum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001395
-name: adult animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001396
-name: aioli
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001397
-name: alcoholic drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001398
-name: algae and related product
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001399
-name: alkaline lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001400
-name: alligator
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001401
-name: almond and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001402
-name: almond tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001403
-name: amaranth and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001404
-name: amphibian and product thereof
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001405
-name: anaerobic mud
-synonym: "anoxic mud" EXACT [TyDI:53789]
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001406
-name: anaerobic sediment
-synonym: "anoxic sediment" EXACT [TyDI:53756]
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001407
-name: animal blood and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001408
-name: animal bone and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001409
-name: animal bone marrow and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001410
-name: animal brain and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001411
-name: animal foot and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001412
-name: animal head and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001413
-name: animal heart and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001414
-name: animal kidney and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001415
-name: animal liver and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001416
-name: animal manure
-is_a: OBT:000985 ! animal waste
-
-[Term]
-id: OBT:001417
-name: animal marrowbone
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001418
-name: animal neck and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001419
-name: animal roe and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001420
-name: animal skin and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001421
-name: animal stomach and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001422
-name: animal tail and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001423
-name: animal tongue and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001424
-name: ant
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001425
-name: anther
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001426
-name: anther part
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001427
-name: aorta
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001428
-name: aphid
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001429
-name: appendix
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001430
-name: aquatic sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001431
-name: aquifer sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001432
-name: arm
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001433
-name: aromatic product and primary derivative thereof
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001434
-name: arsenate treated wood
-is_a: OBT:001359 ! treated wood
-
-[Term]
-id: OBT:001435
-name: avian crop
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001436
-name: bakery product
-synonym: "baked good" RELATED [TyDI:50595]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001437
-name: basophil
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:001438
-name: beach mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001439
-name: bean and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001440
-name: bechamel sauce
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001441
-name: bee
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001442
-name: berry and small fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001443
-name: bio clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001445
-name: birch
-synonym: "birch tree" EXACT []
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001446
-name: bird
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:001447
-name: bird meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001448
-name: birria
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:001449
-name: black anoxic freshwater mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001450
-name: black sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001451
-name: blade
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001452
-name: blanket bog peat
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001453
-name: blood-feeding insect
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001454
-name: borax leachate
-is_a: OBT:001173 ! leachate
-
-[Term]
-id: OBT:001455
-name: borehole
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001456
-name: bottle
-is_a: OBT:001110 ! food container
-
-[Term]
-id: OBT:001457
-name: brackish pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001458
-name: bran
-is_a: OBT:001209 ! milled food
-
-[Term]
-id: OBT:001459
-name: brassica vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001460
-name: breakfast cereal
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001461
-name: brisket saw
-synonym: "mechanical saw" RELATED [TyDI:57225]
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001462
-name: buckwheat and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001463
-name: bud
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:001464
-name: bug
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001465
-name: bulb vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001466
-name: burger
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001467
-name: butcher's knife
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001468
-name: butter
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001469
-name: buttermilk
-synonym: "butter milk" EXACT [TyDI:57950]
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001470
-name: caecal content
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001471
-name: caecum
-synonym: "cecum" EXACT [TyDI:49664]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001472
-name: can
-synonym: "tin" EXACT []
-is_a: OBT:001110 ! food container
-
-[Term]
-id: OBT:001473
-name: canned food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001474
-name: carr
-is_a: OBT:001344 ! swamp
-
-[Term]
-id: OBT:001475
-name: cashew and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001476
-name: cattle dipping
-synonym: "cattle dip" EXACT [TyDI:50013]
-is_a: OBT:001181 ! liquid agricultural waste
-
-[Term]
-id: OBT:001477
-name: cattle-farm compost
-is_a: OBT:001194 ! manure compost
-
-[Term]
-id: OBT:001478
-name: cereal bar
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001479
-name: cereal grain and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001480
-name: cheese
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001481
-name: cheese rind
-is_a: OBT:001114 ! food rind
-
-[Term]
-id: OBT:001482
-name: cheese smear
-is_a: OBT:001342 ! surface smear
-
-[Term]
-id: OBT:001483
-name: chemical weapons factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001484
-name: chia seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001485
-name: chicken coop
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001486
-name: chopstick
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001487
-name: citrus fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001488
-name: cloaca
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001489
-name: coal mine waste
-synonym: "coal refuse" RELATED [TyDI:53145]
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001490
-name: coal-cleaning residue
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001491
-name: coastal lagoon mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001492
-name: coastal sand
-is_a: OBT:001293 ! sand
-
-[Term]
-id: OBT:001493
-name: cockroach
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001494
-name: cocoa bean and primary derivative thereof
-is_a: OBT:001238 ! oilfruit and primary derivative thereof
-
-[Term]
-id: OBT:001495
-name: coconut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001496
-name: colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001497
-name: concentrated food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001498
-name: conifer
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001499
-name: cooked food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001500
-name: cooled food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001501
-name: corn chip
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001502
-name: corn silage
-is_a: OBT:001136 ! grass silage
-
-[Term]
-id: OBT:001503
-name: corn tortillas
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001504
-name: coronary artery
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001505
-name: cream
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001506
-name: cresote treated wood
-is_a: OBT:001359 ! treated wood
-
-[Term]
-id: OBT:001507
-name: crocodile
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001508
-name: crustacean and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001509
-name: cutlery
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001510
-name: cutting table
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001511
-name: dairy parlour waste
-is_a: OBT:001062 ! dairy farming waste
-
-[Term]
-id: OBT:001512
-name: dairy soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001513
-name: dambo
-is_a: OBT:001121 ! freshwater wetland
-
-[Term]
-id: OBT:001514
-name: dark chocolate
-is_a: OBT:001036 ! chocolate product
-
-[Term]
-id: OBT:001515
-name: dashi
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001516
-name: dead animal
-is_a: OBT:001063 ! dead organism
-
-[Term]
-id: OBT:001517
-name: decaying insect-invaded wood
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001518
-name: decaying marine algae
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001519
-name: deep sea mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001520
-name: dental plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001521
-name: dental root
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001522
-name: dental root canal
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001523
-name: digester sludge
-is_a: OBT:001309 ! sewage sludge
-
-[Term]
-id: OBT:001524
-name: ditch mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001525
-name: domestic sewage
-is_a: OBT:001307 ! sewage
-
-[Term]
-id: OBT:001526
-name: dried food
-synonym: "dehydrated food" RELATED [TyDI:51927]
-synonym: "dry foods" EXACT [TyDI:58297]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001527
-name: dried nut
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001528
-name: drilling mud
-is_a: OBT:001211 ! mine drainage
-
-[Term]
-id: OBT:001529
-name: drilling pipe
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001530
-name: drinking water
-synonym: "potable water" RELATED [TyDI:49686]
-synonym: "water" RELATED [TyDI:49685]
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001531
-name: drosophila
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001532
-name: dry forest humus
-is_a: OBT:001120 ! forest humus
-
-[Term]
-id: OBT:001533
-name: duodenal ulcer
-is_a: OBT:001248 ! peptic ulcer
-
-[Term]
-id: OBT:001534
-name: duodenum
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001535
-name: echinoderm and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001536
-name: egg based dish
-synonym: "egg dish" RELATED [TyDI:49858]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001537
-name: egg white
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001538
-name: egg yolk
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001539
-name: elbow
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001540
-name: electronics device industry
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001541
-name: elkhorn coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001542
-name: elm
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001543
-name: embryo
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001544
-name: eosinophil
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:001546
-name: fermented food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001547
-name: fillet
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001548
-name: fish based dish
-synonym: "fish dish" RELATED [TyDI:49864]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001549
-name: fish meat and fish meat product
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001550
-name: fish soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001551
-name: flaxseed and primary derivative thereof
-synonym: "flax seed" RELATED [TyDI:51195]
-synonym: "linseed" EXACT [TyDI:51196]
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001552
-name: flour
-is_a: OBT:001209 ! milled food
-
-[Term]
-id: OBT:001553
-name: fly
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001554
-name: food blender
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001555
-name: food dicing machine
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001556
-name: food fermentation equipment
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001557
-name: food processing factory
-synonym: "food factory" EXACT [TyDI:49609]
-synonym: "food processing plant" EXACT [TyDI:49608]
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001558
-name: food processing waste
-synonym: "food residue" RELATED []
-is_a: OBT:001157 ! industrial organic waste
-
-[Term]
-id: OBT:001559
-name: food slicing machine
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001560
-name: fore-stomach
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001561
-name: forest tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001562
-name: fossil stromatolite
-is_a: OBT:001024 ! calcereous rock
-
-[Term]
-id: OBT:001563
-name: freshwater mud
-synonym: "fresh water mud" EXACT [TyDI:55552]
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001564
-name: frozen food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001565
-name: fruit based dish
-synonym: "fruit dish" RELATED [TyDI:57284]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001566
-name: fruit rind
-is_a: OBT:001114 ! food rind
-
-[Term]
-id: OBT:001567
-name: fruit tree
-comment: horticole meaning
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:001568
-name: fruit with edible peel and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001569
-name: fruit with inedible peel and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001570
-name: fruiting vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001571
-name: fuel ethanol production facility
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001572
-name: fuel oil piping system
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:001573
-name: fungi and related product
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001574
-name: funicle
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001575
-name: gas piping system
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:001576
-name: gas tank
-synonym: "gas reservoir" EXACT [TyDI:56799]
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001577
-name: gastric mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001578
-name: gazpacho
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001579
-name: geothermal lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001580
-name: geyser
-is_a: OBT:001333 ! spring
-
-[Term]
-id: OBT:001581
-name: gingival sulcus
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001582
-name: gizzard
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001583
-name: glassy rind of lava
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001584
-name: gold mine
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:001585
-name: green tea leaf
-is_a: OBT:001162 ! ingredient for hot drink
-
-[Term]
-id: OBT:001586
-name: grocery
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001587
-name: guano
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001588
-name: hamburger meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001589
-name: hand
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001590
-name: hazelnut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001591
-name: heartwood
-is_a: OBT:001383 ! wood
-
-[Term]
-id: OBT:001592
-name: heat-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001593
-name: hemp seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001594
-name: high temperature oil field
-is_a: OBT:001235 ! oil field
-
-[Term]
-id: OBT:001595
-name: holoplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001596
-name: honey
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:001597
-name: hot dog
-synonym: "hot-dog" EXACT [TyDI:52584]
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001598
-name: hot drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001599
-name: hot mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001600
-name: hydathode
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001601
-name: ileum
-synonym: "ileum of the small intestine" RELATED [TyDI:49566]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001602
-name: intra-uterine progeny
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001603
-name: ionised food
-synonym: "ionized food" EXACT [TyDI:53475]
-synonym: "irradiated food" RELATED [TyDI:53474]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001604
-name: jarred food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001605
-name: jejunum
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001606
-name: jellyfish and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001607
-name: jointvetch
-synonym: "Aeschynomene" EXACT [TyDI:52426]
-is_a: OBT:001247 ! pea family
-
-[Term]
-id: OBT:001608
-name: knee
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001609
-name: larvae
-synonym: "larval" RELATED [TyDI:51296]
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001610
-name: latex processing factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001611
-name: leaf margin
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001612
-name: leafhopper
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001613
-name: leafy vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001614
-name: leech
-is_a: OBT:000987 ! annelid
-
-[Term]
-id: OBT:001615
-name: legume based dish
-synonym: "legume dish" RELATED [TyDI:49764]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001616
-name: legume soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001617
-name: lentil and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001618
-name: lime soap
-is_a: OBT:001324 ! soap
-
-[Term]
-id: OBT:001619
-name: liquid egg product
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001620
-name: litter
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001621
-name: livestock barn
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001622
-name: lupin and related product
-synonym: "lupine" EXACT [TyDI:51239]
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001623
-name: lymphocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:001624
-name: mammal meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001625
-name: mammalian
-synonym: "mammal" RELATED [TyDI:49573]
-synonym: "mammalia" RELATED [TyDI:49572]
-synonym: "mammalia-associated habitat" EXACT [TyDI:49571]
-synonym: "mammalian host" RELATED [TyDI:49574]
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:001626
-name: manufacture
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001627
-name: manure
-is_a: OBT:001181 ! liquid agricultural waste
-
-[Term]
-id: OBT:001628
-name: maple tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001629
-name: marinated food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001630
-name: marine crustacean
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:001631
-name: marine mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001632
-name: market garden plant
-is_a: OBT:001125 ! garden plant
-
-[Term]
-id: OBT:001633
-name: mayonnaise
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001634
-name: meat based dish
-synonym: "meat dish" RELATED [TyDI:49695]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001635
-name: meat hook
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001636
-name: meat juice
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001637
-name: meat soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001638
-name: meatball
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001639
-name: meringue
-is_a: OBT:001045 ! confectionery
-
-[Term]
-id: OBT:001640
-name: meromictic lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001641
-name: meroplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001642
-name: mesenteric artery
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001643
-name: methane seep
-is_a: OBT:001127 ! gas seep
-
-[Term]
-id: OBT:001644
-name: midrib
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001645
-name: milk
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001646
-name: milk chocolate
-is_a: OBT:001036 ! chocolate product
-
-[Term]
-id: OBT:001647
-name: mining slag heap
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001648
-name: mite
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001649
-name: mixed cereal-based snack
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001650
-name: mixed dish
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001651
-name: mollusc and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001652
-name: moth
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001653
-name: mouth
-synonym: "oral" RELATED [TyDI:49560]
-synonym: "oral cavity" RELATED [TyDI:49561]
-is_a: OBT:001020 ! buccal
-
-[Term]
-id: OBT:001654
-name: mucosal surface
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001655
-name: mud sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001656
-name: mudflat
-is_a: OBT:001041 ! coastal wetland
-
-[Term]
-id: OBT:001657
-name: muesli
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001658
-name: mummy tissue
-is_a: OBT:001064 ! dead tissue
-
-[Term]
-id: OBT:001659
-name: mushroom based dish
-synonym: "mushroom dish" RELATED [TyDI:49770]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001660
-name: mustard
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001661
-name: nasopharyngeal mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001662
-name: newborn animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001663
-name: nitrogen fertilizer factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001665
-name: nut
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001666
-name: oak
-synonym: "oak tree" EXACT []
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001668
-name: oesophagus
-synonym: "gullet" EXACT [TyDI:49622]
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001669
-name: offshore oil industry
-is_a: OBT:001236 ! oil industry
-
-[Term]
-id: OBT:001670
-name: offspring
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001671
-name: oil pipeline
-synonym: "petroleum pipeline" RELATED [TyDI:52513]
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001672
-name: oil reservoir
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001673
-name: oil seep
-synonym: "petroleum seep" EXACT [TyDI:53778]
-is_a: OBT:001058 ! crude oil
-
-[Term]
-id: OBT:001674
-name: oil spill
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001675
-name: oil-water separator
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001676
-name: okpehe
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001677
-name: omasum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001678
-name: open pit mine
-synonym: "opencast mine" EXACT [TyDI:52676]
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:001679
-name: orange storehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001680
-name: organic leachate
-is_a: OBT:001173 ! leachate
-
-[Term]
-id: OBT:001681
-name: ornemental tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001682
-name: ovary wall
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001683
-name: ovule
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001684
-name: ovule part
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001685
-name: packaging clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001686
-name: packaging factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001687
-name: packed food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001688
-name: paisa mire
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001689
-name: palagonite rind
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001690
-name: palisade layer
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001691
-name: paper mill
-synonym: "paper factory" EXACT [TyDI:52691]
-synonym: "pulp and paper mill" RELATED [TyDI:52690]
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001692
-name: paper mill sludge
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001693
-name: parasitic nematode
-is_a: OBT:001230 ! nematode
-
-[Term]
-id: OBT:001694
-name: pasta and related product
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001695
-name: pasta based dish
-synonym: "pasta dish" RELATED [TyDI:49790]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001696
-name: pea and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001697
-name: peanut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001698
-name: peat cut
-synonym: "peat cutting" EXACT [TyDI:53772]
-is_a: OBT:001258 ! plant material
-
-[Term]
-id: OBT:001699
-name: peat swamp forest
-synonym: "peat swamp" EXACT [TyDI:53765]
-is_a: OBT:001344 ! swamp
-
-[Term]
-id: OBT:001700
-name: peatland
-synonym: "peat bog" RELATED [TyDI:51535]
-synonym: "peat cutting area" RELATED [TyDI:51533]
-synonym: "peatbog" RELATED [TyDI:51534]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001701
-name: pecan and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001702
-name: pericarp
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001703
-name: periodontal pocket
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001704
-name: periodontium
-synonym: "periodontal" RELATED [TyDI:52665]
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001705
-name: permafrost sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001706
-name: pesto
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001707
-name: petal
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001708
-name: petiole
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001709
-name: petrochemical factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001710
-name: petroleum refinery
-is_a: OBT:001281 ! refinery
-
-[Term]
-id: OBT:001711
-name: petroleum reservoir
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001713
-name: phloem
-is_a: OBT:001370 ! vascular tissue
-
-[Term]
-id: OBT:001714
-name: phytoplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001715
-name: pine forest
-is_a: OBT:003881 ! conifer forest
-
-[Term]
-id: OBT:001716
-name: pine forest humus
-is_a: OBT:001120 ! forest humus
-
-[Term]
-id: OBT:001717
-name: pistachio and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001718
-name: agricultural plant residue
-synonym: "agricultural plant waste" NARROW []
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001719
-name: pocosin
-is_a: OBT:001121 ! freshwater wetland
-
-[Term]
-id: OBT:001720
-name: polar sea ice
-is_a: OBT:001300 ! sea ice
-
-[Term]
-id: OBT:001721
-name: pollen tube
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001722
-name: pome fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001723
-name: poppy seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001724
-name: potato plant
-is_a: OBT:001362 ! tuber
-
-[Term]
-id: OBT:001725
-name: potato based dish
-synonym: "potato dish" RELATED [TyDI:49705]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001726
-name: potato chip
-synonym: "potato crisp" RELATED [TyDI:51417]
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001727
-name: poultry house
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001728
-name: powdered food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001729
-name: pressure treated food
-synonym: "pressure processed food" RELATED [TyDI:53464]
-synonym: "pressure-treated food" RELATED [TyDI:53467]
-synonym: "pressuretreated food" EXACT [TyDI:53465]
-synonym: "pressurized food" RELATED [TyDI:53466]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001730
-name: progeny
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001731
-name: pumpkin seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001732
-name: pupa
-synonym: "pupal" RELATED [TyDI:51317]
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001733
-name: quiche
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001734
-name: quinoa and primary derivative thereof
-synonym: "quinoa seed" EXACT [TyDI:51226]
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001735
-name: raised mire
-synonym: "raised bog" RELATED [TyDI:51528]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001736
-name: raw dough
-synonym: "dough" EXACT [TyDI:50582]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001737
-name: rectal swab
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001738
-name: rectum
-synonym: "rectal" RELATED [TyDI:55347]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001739
-name: red clay
-is_a: OBT:001037 ! clay
-
-[Term]
-id: OBT:001740
-name: red-pigmented bacteriome
-is_a: OBT:000998 ! bacteriome
-
-[Term]
-id: OBT:001741
-name: reef
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001742
-name: reptile and product thereof
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001743
-name: reticulum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001744
-name: rice based dish
-synonym: "rice dish" RELATED [TyDI:49793]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001745
-name: rice chip
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001746
-name: roasted coffee bean
-is_a: OBT:001162 ! ingredient for hot drink
-
-[Term]
-id: OBT:001747
-name: root and tuber vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001748
-name: rotting hay
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001749
-name: rumen
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001750
-name: rye grass silage
-is_a: OBT:001136 ! grass silage
-
-[Term]
-id: OBT:001751
-name: saline sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001752
-name: salivary gland
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001753
-name: salt
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001754
-name: salt lake mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001755
-name: salt-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001756
-name: sandwich
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001757
-name: sandy sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001758
-name: sausage
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001759
-name: saw mill
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001760
-name: scleractinian coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001761
-name: sea sand
-is_a: OBT:001293 ! sand
-
-[Term]
-id: OBT:001762
-name: seafood based dish
-synonym: "seafood dish" RELATED [TyDI:49781]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001763
-name: seagrass
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001764
-name: sedimentation pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001765
-name: seed
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001766
-name: seed part
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001767
-name: sepal
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001768
-name: sesame seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001769
-name: shallow pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001770
-name: shoe factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001771
-name: shrub
-is_a: OBT:001125 ! garden plant
-
-[Term]
-id: OBT:001772
-name: sigmoid colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001773
-name: sludge
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001774
-name: smoked food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001775
-name: smooth cord grass
-synonym: "Spartina alterniflora" EXACT [TyDI:50533]
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001776
-name: snail
-is_a: OBT:001215 ! mollusc
-
-[Term]
-id: OBT:001777
-name: snake
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001778
-name: soda
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001779
-name: soft drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001780
-name: solar lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001781
-name: soybean and related product
-synonym: "soy and related product" RELATED [TyDI:51059]
-synonym: "soyabean and related product" RELATED [TyDI:51060]
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001782
-name: spacecraft assembly clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001783
-name: sphagnum bog
-synonym: "acidic Sphagnum peat bog" RELATED [TyDI:52686]
-synonym: "Sphagnum peat bog" RELATED [TyDI:52687]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001784
-name: spice
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001785
-name: spider
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001786
-name: stall
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001787
-name: star coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001788
-name: stem cortex part
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:001789
-name: stem vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001790
-name: stigma
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001791
-name: stink bug
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001792
-name: stomach
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001793
-name: stomach mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001794
-name: stomach ulcer
-is_a: OBT:001248 ! peptic ulcer
-
-[Term]
-id: OBT:001795
-name: stomata
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001796
-name: stone fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001797
-name: stratified lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001798
-name: style
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001799
-name: subgingiva
-synonym: "subgingival" RELATED [TyDI:57906]
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001800
-name: subgingival plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001801
-name: submarine basalt
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001802
-name: sugar confectionery
-synonym: "candy" RELATED [TyDI:57248]
-is_a: OBT:001045 ! confectionery
-
-[Term]
-id: OBT:001803
-name: sugar-beet plant
-synonym: "betroot plant" EXACT [TyDI:49625]
-is_a: OBT:001362 ! tuber
-
-[Term]
-id: OBT:001804
-name: sugar-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001805
-name: sunflower seed and primary derivatives thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001806
-name: supragingival plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001807
-name: surface sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001808
-name: sweet clover
-synonym: "Melilotus albus" EXACT [TyDI:52622]
-is_a: OBT:001247 ! pea family
-
-[Term]
-id: OBT:001809
-name: swine house
-synonym: "swine barn" RELATED [TyDI:57772]
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001810
-name: tannery
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001811
-name: tannery sludge
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001812
-name: tea tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001813
-name: terminal ileum
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001814
-name: termite
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001815
-name: terrestrial crustacean
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:001816
-name: terrestrial invertebrate product
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001817
-name: textile dye effluent
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001818
-name: textile mill
-synonym: "textile factory" NARROW []
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001819
-name: thermal power plant
-is_a: OBT:001264 ! power plant
-
-[Term]
-id: OBT:001820
-name: thermal spring
-is_a: OBT:001333 ! spring
-
-[Term]
-id: OBT:001821
-name: tick
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001822
-name: tobacco warehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001823
-name: toe
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001824
-name: tomato ketchup
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001825
-name: tongue
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001826
-name: tooth
-synonym: "dental" EXACT [TyDI:52708]
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001827
-name: toothpick
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001828
-name: tortoise
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001829
-name: transverse colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001830
-name: tundra mire
-synonym: "subarctic mire" RELATED [TyDI:53775]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001831
-name: tunicate and product thereof
-synonym: "sea squirt" RELATED [TyDI:49810]
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001832
-name: turtle
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001833
-name: vaginal swab
-is_a: OBT:001369 ! vaginal secretion
-
-[Term]
-id: OBT:001834
-name: vegetable based dish
-synonym: "vegetable dish" RELATED [TyDI:49776]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001835
-name: vein
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001836
-name: vestibular mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001837
-name: vitamin supplement
-is_a: OBT:001070 ! dietary supplement
-
-[Term]
-id: OBT:001838
-name: walnut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001839
-name: war readiness warehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001840
-name: wasp
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001841
-name: water based beverage
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001842
-name: water based dish
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001843
-name: water dispenser
-is_a: OBT:001082 ! drinking water supply
-
-[Term]
-id: OBT:001844
-name: water in cooling tower
-is_a: OBT:001047 ! cooling water
-
-[Term]
-id: OBT:001845
-name: weed
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001846
-name: whey
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001847
-name: whole egg
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001848
-name: xylem
-is_a: OBT:001370 ! vascular tissue
-
-[Term]
-id: OBT:001849
-name: young animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001850
-name: zinc factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001851
-name: zooplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001852
-name: Aeschynomene indica
-is_a: OBT:001607 ! jointvetch
-
-[Term]
-id: OBT:001853
-name: Arabidopsis thaliana
-is_a: OBT:001390 ! Arabidopsis
-
-[Term]
-id: OBT:001854
-name: Intertidal sand
-is_a: OBT:001492 ! coastal sand
-
-[Term]
-id: OBT:001855
-name: UHT food
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:001856
-name: activated sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001857
-name: agricultural soil
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:001858
-name: algae as food
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:001859
-name: almond as food
-is_a: OBT:001401 ! almond and primary derivative thereof
-
-[Term]
-id: OBT:001860
-name: amaranth
-is_a: OBT:001403 ! amaranth and primary derivative thereof
-
-[Term]
-id: OBT:001861
-name: anaerobic digester sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001862
-name: anaerobic sewage sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001863
-name: animal blood
-is_a: OBT:001407 ! animal blood and product thereof
-
-[Term]
-id: OBT:001864
-name: animal bone
-is_a: OBT:001408 ! animal bone and product thereof
-
-[Term]
-id: OBT:001865
-name: animal brain
-is_a: OBT:001410 ! animal brain and product thereof
-
-[Term]
-id: OBT:001866
-name: animal foot
-is_a: OBT:001411 ! animal foot and product thereof
-
-[Term]
-id: OBT:001867
-name: animal head
-is_a: OBT:001412 ! animal head and product thereof
-
-[Term]
-id: OBT:001868
-name: animal heart
-is_a: OBT:001413 ! animal heart and product thereof
-
-[Term]
-id: OBT:001869
-name: animal kidney
-is_a: OBT:001414 ! animal kidney and product thereof
-
-[Term]
-id: OBT:001870
-name: animal liver
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:001871
-name: animal neck
-is_a: OBT:001418 ! animal neck and product thereof
-
-[Term]
-id: OBT:001872
-name: animal roe
-is_a: OBT:001419 ! animal roe and product thereof
-
-[Term]
-id: OBT:001873
-name: animal skin
-is_a: OBT:001420 ! animal skin and product thereof
-
-[Term]
-id: OBT:001874
-name: animal stomach
-is_a: OBT:001421 ! animal stomach and product thereof
-
-[Term]
-id: OBT:001875
-name: animal tail
-is_a: OBT:001422 ! animal tail and product thereof
-
-[Term]
-id: OBT:001876
-name: animal tongue
-is_a: OBT:001423 ! animal tongue and product thereof
-
-[Term]
-id: OBT:001877
-name: anoxic sewage sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001878
-name: antelope
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001879
-name: apple and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:001880
-name: apple tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001881
-name: apricot and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:001882
-name: armadillo
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001883
-name: artichoke and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001884
-name: arugula
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001885
-name: aspargus and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001886
-name: aubergine and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001887
-name: avocado and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:001888
-name: baby corn and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001889
-name: baked food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001890
-name: bamboo shoot and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001891
-name: banana and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:001892
-name: banana tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001893
-name: barley and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:001894
-name: basil and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001895
-name: bat
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001896
-name: beach sand
-is_a: OBT:001492 ! coastal sand
-
-[Term]
-id: OBT:001897
-name: bean
-is_a: OBT:001439 ! bean and related product
-
-[Term]
-id: OBT:001898
-name: bear
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001899
-name: beef
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:001900
-name: beetroot and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001901
-name: berry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001902
-name: biscuit
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001903
-name: blackberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001904
-name: blackcurrant and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001905
-name: blanched food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001906
-name: blood sausage
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:001907
-name: blueberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001908
-name: boiled food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001909
-name: bottled water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:001910
-name: bottling factory
-is_a: OBT:001686 ! packaging factory
-
-[Term]
-id: OBT:001911
-name: bouillabaisse
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:001912
-name: bovine milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001913
-name: bread
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001914
-name: bread pre mix
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:001915
-name: broccoli and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001916
-name: brussel sprout and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001917
-name: buckwheat
-is_a: OBT:001462 ! buckwheat and primary derivative thereof
-
-[Term]
-id: OBT:001918
-name: buffalo milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001919
-name: bumblebee
-is_a: OBT:001441 ! bee
-
-[Term]
-id: OBT:001920
-name: bun
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001921
-name: cake pre mix
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:001922
-name: calf barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001923
-name: camel
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001924
-name: camel milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001925
-name: canal of root filled tooth
-is_a: OBT:001522 ! dental root canal
-
-[Term]
-id: OBT:001926
-name: candied food
-is_a: OBT:001804 ! sugar-preserved food
-
-[Term]
-id: OBT:001927
-name: canned fish
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001928
-name: canned meat
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001929
-name: canned seafood
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001930
-name: canning factory
-is_a: OBT:001686 ! packaging factory
-
-[Term]
-id: OBT:001931
-name: cantaloupe rind
-synonym: "cantaloupe surface" RELATED [TyDI:57986]
-is_a: OBT:001566 ! fruit rind
-
-[Term]
-id: OBT:001932
-name: caramel
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:001933
-name: cardoon and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001934
-name: carrot and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001935
-name: cashew apple
-is_a: OBT:001475 ! cashew and primary derivative thereof
-
-[Term]
-id: OBT:001936
-name: cashew seed
-is_a: OBT:001475 ! cashew and primary derivative thereof
-
-[Term]
-id: OBT:001937
-name: cauliflower and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001938
-name: celeriac and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001939
-name: celery and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001940
-name: celery leaf and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001941
-name: cep and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:001942
-name: ceviche
-synonym: "cebiche" EXACT [TyDI:57281]
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:001943
-name: chard and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001944
-name: cheese brine
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:001945
-name: cheeseburger
-is_a: OBT:001466 ! burger
-
-[Term]
-id: OBT:001946
-name: cherry and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:001947
-name: chewing gum
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:001948
-name: chia seed
-is_a: OBT:001484 ! chia seed and primary derivative thereof
-
-[Term]
-id: OBT:001949
-name: chicken house
-is_a: OBT:001727 ! poultry house
-
-[Term]
-id: OBT:001950
-name: chili pepper and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001951
-name: chinese cabbage and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001952
-name: chipolata
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:001953
-name: chive and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001954
-name: cinnamon and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001955
-name: citronella grass and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001956
-name: citrus tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001957
-name: clove and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001958
-name: coal spoil heap
-is_a: OBT:001489 ! coal mine waste
-
-[Term]
-id: OBT:001959
-name: cocktail drink
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:001960
-name: cocoa
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001961
-name: cocoa bean
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001962
-name: cocoa beverage
-is_a: OBT:001598 ! hot drink
-
-[Term]
-id: OBT:001963
-name: cocoa butter
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001964
-name: cocoa powder
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001965
-name: coconut as food
-is_a: OBT:001495 ! coconut and primary derivative thereof
-
-[Term]
-id: OBT:001966
-name: coffee beverage
-is_a: OBT:001598 ! hot drink
-
-[Term]
-id: OBT:001967
-name: collard green
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001968
-name: common mushroom and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:001969
-name: compote
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:001970
-name: contaminated drinking water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:001971
-name: cooked fish
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:001972
-name: courgette and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001973
-name: couscous
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:001974
-name: cow barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001975
-name: cow milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001976
-name: crab
-is_a: OBT:001630 ! marine crustacean
-
-[Term]
-id: OBT:001977
-name: crab and product thereof
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:001978
-name: cracker
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001979
-name: cranberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001980
-name: crocodile product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:001981
-name: cucumber and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001982
-name: cultivated field
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:001983
-name: cumin
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:001984
-name: cured food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:001985
-name: curry powder
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:001986
-name: cuttlefish and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:001987
-name: dairy barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001988
-name: dairy processing plant
-synonym: "dairy factory" EXACT []
-synonym: "milk processing factory" RELATED [TyDI:55159]
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:001989
-name: date and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:001990
-name: date palm tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001991
-name: dead body
-is_a: OBT:001516 ! dead animal
-
-[Term]
-id: OBT:001995
-name: deteriorated canned food
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001996
-name: diadromous fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002000
-name: dough mixer
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002001
-name: dragee
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002002
-name: dried animal product
-is_a: OBT:001526 ! dried food
-
-[Term]
-id: OBT:002003
-name: dried bean
-is_a: OBT:001439 ! bean and related product
-
-[Term]
-id: OBT:002004
-name: dried lentil
-is_a: OBT:001617 ! lentil and related product
-
-[Term]
-id: OBT:002005
-name: dried pasta
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002006
-name: dried pea
-is_a: OBT:001696 ! pea and related product
-
-[Term]
-id: OBT:002007
-name: dried plant product
-is_a: OBT:001526 ! dried food
-
-[Term]
-id: OBT:002008
-name: dried seaweed
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:002009
-name: duck egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002010
-name: durian and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002011
-name: earthworm-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002012
-name: egg sac
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002013
-name: egg sac part
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002014
-name: embryo
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002015
-name: embryo part
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002016
-name: endosperm
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002017
-name: enriched dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002018
-name: environmental water with chemical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002019
-name: environmental water with physical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002020
-name: equine meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002021
-name: escarole and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002022
-name: ewe milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002023
-name: farmed fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002024
-name: fennel and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002025
-name: fermentation vat
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002026
-name: ferret
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002027
-name: fig and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:002028
-name: filarial nematode
-is_a: OBT:001693 ! parasitic nematode
-
-[Term]
-id: OBT:002029
-name: fir tree
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002030
-name: fish farming pond
-is_a: OBT:000046 ! aquaculture pond
-is_a: OBT:000093 ! fish pond
-
-[Term]
-id: OBT:002031
-name: fish sashimi
-synonym: "sashimi" RELATED [TyDI:54621]
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:002032
-name: fish-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002033
-name: flaxseed
-is_a: OBT:001551 ! flaxseed and primary derivative thereof
-
-[Term]
-id: OBT:002034
-name: flea
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002036
-name: fluvial dambo
-is_a: OBT:001513 ! dambo
-
-[Term]
-id: OBT:002037
-name: foie gras
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:002038
-name: folivorous bird
-synonym: "leaf-eating bird" EXACT [TyDI:56639]
-synonym: "leaves-eating bird" EXACT [TyDI:56640]
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002039
-name: food fermentation factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002040
-name: fork as utensil
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002041
-name: fowl
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002042
-name: fresh animal manure
-is_a: OBT:001416 ! animal manure
-
-[Term]
-id: OBT:002043
-name: fresh cheese
-is_a: OBT:001480 ! cheese
-
-[Term]
-id: OBT:002044
-name: fresh pasta
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002045
-name: freshwater fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002046
-name: freshwater sediment
-is_a: OBT:001430 ! aquatic sediment
-
-[Term]
-id: OBT:002047
-name: fried food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002048
-name: fried rice
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002049
-name: frikadeller
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002050
-name: frog product
-is_a: OBT:001404 ! amphibian and product thereof
-
-[Term]
-id: OBT:002051
-name: fruit fly
-synonym: "Drosophila" EXACT [TyDI:56449]
-is_a: OBT:001553 ! fly
-
-[Term]
-id: OBT:002052
-name: fruit salad
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:002053
-name: fruit smoothie
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:002054
-name: fruit-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002055
-name: fungi as food
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002056
-name: game bird meat
-synonym: "bushmeat bird meat" EXACT [TyDI:54008]
-synonym: "wild feathered game" EXACT [TyDI:54009]
-is_a: OBT:001447 ! bird meat
-
-[Term]
-id: OBT:002057
-name: game mammal meat
-synonym: "wild meat" EXACT [TyDI:55569]
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002058
-name: garlic and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002059
-name: geese egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002060
-name: gherkin and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002061
-name: ginger and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002062
-name: glassy rind of seafloor basalt
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002063
-name: gnocchi
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002064
-name: goat meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002065
-name: goat milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002066
-name: grape and primary derivative thereof
-synonym: "grape" EXACT [TyDI:51423]
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002067
-name: grape leaf and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002068
-name: griddled food
-synonym: "griddle cooked food" EXACT [TyDI:53310]
-synonym: "griddle-cooked food" EXACT [TyDI:53309]
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002069
-name: grilled food
-synonym: "barbecued food" EXACT [TyDI:52528]
-synonym: "broiled food" RELATED [TyDI:52529]
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002070
-name: gum drop
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002071
-name: hamburger
-is_a: OBT:001466 ! burger
-
-[Term]
-id: OBT:002072
-name: hard tick
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002073
-name: hay
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002074
-name: hazelnut
-is_a: OBT:001590 ! hazelnut and primary derivative thereof
-
-[Term]
-id: OBT:002075
-name: head cabbage and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:002076
-name: hemp seed
-is_a: OBT:001593 ! hemp seed and primary derivative thereof
-
-[Term]
-id: OBT:002077
-name: hen egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002078
-name: herbivore
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002079
-name: high pressure treated food
-synonym: "high-pressure-treated food" RELATED [TyDI:53457]
-is_a: OBT:001729 ! pressure treated food
-
-[Term]
-id: OBT:002080
-name: honey bee
-is_a: OBT:001441 ! bee
-
-[Term]
-id: OBT:002081
-name: horseradish and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002082
-name: hospital equipment
-is_a: OBT:000097 ! hospital environment
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:002083
-name: human milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002084
-name: ice tea
-is_a: OBT:001841 ! water based beverage
-
-[Term]
-id: OBT:002085
-name: ice-cream factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002086
-name: industrial bakery
-synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:003759 ! bakery
-
-[Term]
-id: OBT:002087
-name: insect product
-is_a: OBT:001816 ! terrestrial invertebrate product
-
-[Term]
-id: OBT:002088
-name: integument
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002089
-name: jam
-is_a: OBT:001804 ! sugar-preserved food
-
-[Term]
-id: OBT:002090
-name: kaki and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:002091
-name: kiwi and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002092
-name: knife
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002093
-name: kombu
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:002094
-name: kombucha
-is_a: OBT:001841 ! water based beverage
-
-[Term]
-id: OBT:002095
-name: lamb meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002096
-name: landfill leachate
-is_a: OBT:001680 ! organic leachate
-
-[Term]
-id: OBT:002097
-name: lasagna
-is_a: OBT:001695 ! pasta based dish
-
-[Term]
-id: OBT:002098
-name: laurel and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002099
-name: lavander and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002100
-name: lean dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002101
-name: leek and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002102
-name: left arm
-is_a: OBT:001432 ! arm
-
-[Term]
-id: OBT:002103
-name: lemon and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002104
-name: lentil
-is_a: OBT:001617 ! lentil and related product
-
-[Term]
-id: OBT:002105
-name: lettuce and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002106
-name: lime and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002107
-name: liqueur
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002108
-name: liquid egg mixed
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002109
-name: liquid egg white
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002110
-name: liquid egg yolk
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002111
-name: litchi and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002112
-name: lizard product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002113
-name: lobster
-is_a: OBT:001630 ! marine crustacean
-
-[Term]
-id: OBT:002114
-name: lobster and product thereof
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:002115
-name: loukoumi
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002116
-name: louse
-synonym: "lice" EXACT [TyDI:50227]
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002117
-name: low salinity mud flat sediment
-is_a: OBT:001655 ! mud sediment
-
-[Term]
-id: OBT:002118
-name: lupin
-synonym: "lupine" EXACT [TyDI:51239]
-is_a: OBT:001622 ! lupin and related product
-
-[Term]
-id: OBT:002119
-name: lupin seed
-is_a: OBT:001622 ! lupin and related product
-
-[Term]
-id: OBT:002120
-name: maize and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002121
-name: mandarin and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002122
-name: mango and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002123
-name: mare milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002124
-name: marine anoxic mud
-is_a: OBT:001631 ! marine mud
-
-[Term]
-id: OBT:002125
-name: marine black mud
-is_a: OBT:001631 ! marine mud
-
-[Term]
-id: OBT:002126
-name: marine fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002127
-name: marine sediment
-synonym: "pelagic sediment \{alternative name\}" EXACT [TyDI:56108]
-is_a: OBT:001430 ! aquatic sediment
-
-[Term]
-id: OBT:002128
-name: marshmallow
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002129
-name: meat processing plant
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002130
-name: meat patty
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002131
-name: meat sashimi
-synonym: "sashimi" RELATED [TyDI:54621]
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002132
-name: melon and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002133
-name: merguez
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:002134
-name: micropyle
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002135
-name: mid-ocean ridge basalt
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002136
-name: milk product
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002137
-name: millet and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002138
-name: mint and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002139
-name: mixed vegetable
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:002140
-name: modified-atmosphere-packed food
-is_a: OBT:001687 ! packed food
-
-[Term]
-id: OBT:002141
-name: morel and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002142
-name: mosquito
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002143
-name: moussaka
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002144
-name: mucocutaneous surface
-is_a: OBT:001654 ! mucosal surface
-
-[Term]
-id: OBT:002145
-name: mulberry tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002146
-name: mummy
-is_a: OBT:001516 ! dead animal
-
-[Term]
-id: OBT:002147
-name: mussel and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002148
-name: mustelidae
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002149
-name: mutton meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002150
-name: nectarine and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002151
-name: nougat
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002152
-name: nucellus
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002153
-name: nutmeg
-synonym: "Myristica fragrans" EXACT [TyDI:54728]
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:002154
-name: oat and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002155
-name: octopus and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002156
-name: oil sludge
-is_a: OBT:001773 ! sludge
-
-[Term]
-id: OBT:002157
-name: okra and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002158
-name: oleander
-is_a: OBT:001771 ! shrub
-
-[Term]
-id: OBT:002159
-name: olive tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002160
-name: onion and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002161
-name: opossum
-synonym: "didelphidae" RELATED [TyDI:54144]
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002162
-name: orange and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002163
-name: orange tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002164
-name: oregano and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002165
-name: oyster and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002166
-name: paella
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002167
-name: palm heart and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002168
-name: paper manufacture
-is_a: OBT:001626 ! manufacture
-
-[Term]
-id: OBT:002169
-name: parrot
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002170
-name: parsley and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002171
-name: parsnip and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002172
-name: passerine bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002173
-name: pasteurized food
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:002174
-name: pastry product
-synonym: "pastry" RELATED [TyDI:51162]
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:002175
-name: pea
-is_a: OBT:001696 ! pea and related product
-
-[Term]
-id: OBT:002176
-name: peach and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002177
-name: peanut as food
-is_a: OBT:001697 ! peanut and primary derivative thereof
-
-[Term]
-id: OBT:002178
-name: peanut butter
-is_a: OBT:001697 ! peanut and primary derivative thereof
-
-[Term]
-id: OBT:002179
-name: pear and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:002180
-name: pear tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002181
-name: pecan
-is_a: OBT:001701 ! pecan and primary derivative thereof
-
-[Term]
-id: OBT:002182
-name: pepper
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:002184
-name: pickled food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:002185
-name: pie
-is_a: OBT:001650 ! mixed dish
-
-[Term]
-id: OBT:002186
-name: pigeon
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002187
-name: pine
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002188
-name: pineapple and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002189
-name: pistachio
-is_a: OBT:001717 ! pistachio and primary derivative thereof
-
-[Term]
-id: OBT:002190
-name: plant cutting
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002191
-name: plum and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002192
-name: plum tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002193
-name: poached food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002194
-name: pollen
-is_a: OBT:001426 ! anther part
-
-[Term]
-id: OBT:002195
-name: poppy seed
-is_a: OBT:001723 ! poppy seed and primary derivative thereof
-
-[Term]
-id: OBT:002196
-name: pork
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002197
-name: potato and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002198
-name: poultry litter
-is_a: OBT:001620 ! litter
-
-[Term]
-id: OBT:002199
-name: poultry meat
-is_a: OBT:001447 ! bird meat
-
-[Term]
-id: OBT:002200
-name: prawn and product thereof
-synonym: "shrimp" RELATED [TyDI:56014]
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:002201
-name: primate
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002202
-name: processed cheese
-is_a: OBT:001480 ! cheese
-
-[Term]
-id: OBT:002203
-name: public bathing facility
-is_a: OBT:000050 ! artificial water environment
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:002204
-name: pudding
-is_a: OBT:001650 ! mixed dish
-
-[Term]
-id: OBT:002205
-name: pumpkin and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002206
-name: pumpkin seed
-is_a: OBT:001731 ! pumpkin seed and primary derivative thereof
-
-[Term]
-id: OBT:002207
-name: quail egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002208
-name: quince and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:002209
-name: quinoa
-is_a: OBT:001734 ! quinoa and primary derivative thereof
-
-[Term]
-id: OBT:002210
-name: rabbit meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002211
-name: rabbit tick
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002215
-name: radish and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002216
-name: radish as food
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:002217
-name: radish plant
-is_a: OBT:001391 ! Brassica
-
-[Term]
-id: OBT:002218
-name: raspberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002219
-name: ratatouille
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:002220
-name: redcurrant and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002221
-name: reheated food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002222
-name: rhubarb and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002223
-name: rice and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002224
-name: rice pudding
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002225
-name: rice-plant residue
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002226
-name: right arm
-is_a: OBT:001432 ! arm
-
-[Term]
-id: OBT:002227
-name: ripened sausage
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:002228
-name: roasted food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002229
-name: rocket and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002230
-name: rodent
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002231
-name: rosemary and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002232
-name: rum
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002233
-name: rye and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002234
-name: sage and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002235
-name: sake
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002236
-name: saline brine sediment
-is_a: OBT:001751 ! saline sediment
-
-[Term]
-id: OBT:002237
-name: salsify and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002238
-name: salted food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:002239
-name: sashimi
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:002240
-name: scalded food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002241
-name: sea cucumber and product thereof
-is_a: OBT:001535 ! echinoderm and product thereof
-
-[Term]
-id: OBT:002242
-name: sea pineapple and product thereof
-synonym: "hoya" RELATED [TyDI:54865]
-synonym: "maboya" RELATED [TyDI:54864]
-synonym: "meongge" RELATED [TyDI:54863]
-is_a: OBT:001831 ! tunicate and product thereof
-
-[Term]
-id: OBT:002243
-name: sea salt
-is_a: OBT:001753 ! salt
-
-[Term]
-id: OBT:002244
-name: seed eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002245
-name: sesame oil
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-
-[Term]
-id: OBT:002246
-name: sesame seed
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-
-[Term]
-id: OBT:002247
-name: shallot and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002248
-name: sharpshooter
-is_a: OBT:001612 ! leafhopper
-
-[Term]
-id: OBT:002249
-name: simmered food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002250
-name: slash pine forest
-is_a: OBT:001715 ! pine forest
-
-[Term]
-id: OBT:002251
-name: slaughter plant
-synonym: "abattoir" RELATED [TyDI:50262]
-synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:002129 ! meat processing plant
-
-[Term]
-id: OBT:002252
-name: slaughtering waste
-synonym: "abattoir waste" RELATED [TyDI:52683]
-is_a: OBT:001558 ! food processing waste
-
-[Term]
-id: OBT:002253
-name: snail product
-is_a: OBT:001816 ! terrestrial invertebrate product
-
-[Term]
-id: OBT:002254
-name: snake product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002255
-name: soap scum
-is_a: OBT:001618 ! lime soap
-
-[Term]
-id: OBT:002256
-name: soft tick
-synonym: "soft-bodied tick" EXACT [TyDI:50335]
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002257
-name: soil with chemical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:002258
-name: soil with physical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:002259
-name: soybean
-synonym: "soy" RELATED [TyDI:53483]
-synonym: "soya bean" RELATED [TyDI:53482]
-is_a: OBT:001781 ! soybean and related product
-
-[Term]
-id: OBT:002260
-name: spinach and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002261
-name: spirit
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002262
-name: spoon
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002263
-name: spruce
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002264
-name: squid and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002265
-name: stable manure
-is_a: OBT:001416 ! animal manure
-
-[Term]
-id: OBT:002266
-name: steak tartare
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002267
-name: steamed food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002268
-name: sterilized food
-synonym: "sterilised food" EXACT [TyDI:52554]
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:002269
-name: stewed food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002270
-name: storage box
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002271
-name: straw
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002272
-name: strawberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002273
-name: striploin
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002274
-name: submarine glassy basalt
-synonym: "submarine basalt glass" EXACT [TyDI:57953]
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002275
-name: sugar factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002276
-name: sunflower seed
-is_a: OBT:001805 ! sunflower seed and primary derivatives thereof
-
-[Term]
-id: OBT:002277
-name: surimi
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002278
-name: swede and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002279
-name: sweet corn and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002280
-name: sweet dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002281
-name: sweet pepper and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002282
-name: sweet potato and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002283
-name: tap water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:002284
-name: tarragon and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002285
-name: teff and primary derivative thereof
-synonym: "tef" EXACT [TyDI:51219]
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002286
-name: tenderloin
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002287
-name: testa
-synonym: "seed coat" RELATED [TyDI:56238]
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002288
-name: testa part
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002291
-name: thyme and related product
-synonym: "Thymus vulgaris" RELATED [TyDI:57449]
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002292
-name: tidal mudflat
-synonym: "intertidal mudflat" RELATED [TyDI:58218]
-synonym: "tidal flat" RELATED [TyDI:58217]
-is_a: OBT:001656 ! mudflat
-
-[Term]
-id: OBT:002293
-name: tomato and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002294
-name: tomato plant
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:002295
-name: triticale and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002296
-name: truffle and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002297
-name: turnip and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002298
-name: turtle product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002299
-name: urchin and product thereof
-is_a: OBT:001535 ! echinoderm and product thereof
-
-[Term]
-id: OBT:002300
-name: vacuum-packed food
-is_a: OBT:001687 ! packed food
-
-[Term]
-id: OBT:002301
-name: viennoiserie
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:002302
-name: walnut
-is_a: OBT:001838 ! walnut and primary derivative thereof
-
-[Term]
-id: OBT:002303
-name: walnut oil
-is_a: OBT:001838 ! walnut and primary derivative thereof
-
-[Term]
-id: OBT:002304
-name: wasabi and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002305
-name: watercress and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002306
-name: watermelon and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002307
-name: watermelon rind
-is_a: OBT:001566 ! fruit rind
-
-[Term]
-id: OBT:002308
-name: weatherfish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002309
-name: wheat and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002310
-name: white mustard and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002311
-name: wild fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002312
-name: winter savory and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002313
-name: witloof and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002314
-name: wood tick
-synonym: "American dog tick" EXACT [TyDI:54022]
-synonym: "Dermacentor variabilis" EXACT [TyDI:54020]
-synonym: "Ixodes ricinus" EXACT [TyDI:54021]
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002315
-name: yak
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002316
-name: yak milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002317
-name: yam and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002318
-name: zebra
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002319
-name: American cheese
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002320
-name: Cancoillotte
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002321
-name: Chinese cabbage
-is_a: OBT:001951 ! chinese cabbage and related product
-
-[Term]
-id: OBT:002322
-name: Crème de Brie de Meaux
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002323
-name: Danish pastry
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002324
-name: Drosophila melanogaster
-is_a: OBT:002051 ! fruit fly
-
-[Term]
-id: OBT:002325
-name: Kiri
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002326
-name: Knieküchle
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002327
-name: Ornithodoros moubata
-is_a: OBT:002256 ! soft tick
-
-[Term]
-id: OBT:002328
-name: Ornithodoros turicatae
-is_a: OBT:002256 ! soft tick
-
-[Term]
-id: OBT:002329
-name: The Laughing Cow
-synonym: "La Vache qui Rit" EXACT [TyDI:55418]
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002333
-name: Vienna bread
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002334
-name: anchovie meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002335
-name: anglerfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002336
-name: animal filarial nematode
-is_a: OBT:002028 ! filarial nematode
-
-[Term]
-id: OBT:002340
-name: aphotic zone
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002341
-name: apple as food
-synonym: "apple" EXACT [TyDI:50312]
-is_a: OBT:001879 ! apple and primary derivative thereof
-
-[Term]
-id: OBT:002342
-name: apricot as food
-synonym: "apricot" EXACT [TyDI:50271]
-is_a: OBT:001881 ! apricot and primary derivative thereof
-
-[Term]
-id: OBT:002343
-name: arable soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002344
-name: arctic marine sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002345
-name: artichoke
-is_a: OBT:001883 ! artichoke and related product
-
-[Term]
-id: OBT:002346
-name: asparagus
-is_a: OBT:001885 ! aspargus and related product
-
-[Term]
-id: OBT:002347
-name: aubergine
-is_a: OBT:001886 ! aubergine and related product
-
-[Term]
-id: OBT:002348
-name: avocado as food
-synonym: "avocado" EXACT [TyDI:50236]
-is_a: OBT:001887 ! avocado and primary derivative thereof
-
-[Term]
-id: OBT:002349
-name: baboon
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002350
-name: baby corn
-is_a: OBT:001888 ! baby corn and related product
-
-[Term]
-id: OBT:002351
-name: bacon
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002352
-name: bamboo shoot
-is_a: OBT:001890 ! bamboo shoot and related product
-
-[Term]
-id: OBT:002353
-name: banana as food
-synonym: "banana" EXACT [TyDI:50244]
-is_a: OBT:001891 ! banana and primary derivative thereof
-
-[Term]
-id: OBT:002354
-name: barb meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002355
-name: barley product
-is_a: OBT:001893 ! barley and primary derivative thereof
-
-[Term]
-id: OBT:002356
-name: barracuda meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002357
-name: basil
-is_a: OBT:001894 ! basil and related product
-
-[Term]
-id: OBT:002358
-name: beaver
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002359
-name: beefsteak
-synonym: "beef steak" EXACT [TyDI:53992]
-synonym: "steak" RELATED [TyDI:53991]
-is_a: OBT:001899 ! beef
-
-[Term]
-id: OBT:002360
-name: beer-bottling plant
-is_a: OBT:001910 ! bottling factory
-
-[Term]
-id: OBT:002361
-name: beetroot
-is_a: OBT:001900 ! beetroot and related product
-
-[Term]
-id: OBT:002362
-name: berry as food
-synonym: "berry" EXACT [TyDI:54527]
-is_a: OBT:001901 ! berry and primary derivative thereof
-
-[Term]
-id: OBT:002363
-name: bison meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002364
-name: black anoxic marine sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002365
-name: black pepper
-is_a: OBT:002182 ! pepper
-
-[Term]
-id: OBT:002366
-name: black pudding
-is_a: OBT:001906 ! blood sausage
-
-[Term]
-id: OBT:002367
-name: blackberry as food
-synonym: "blackberry" EXACT [TyDI:50341]
-is_a: OBT:001903 ! blackberry and primary derivative thereof
-
-[Term]
-id: OBT:002368
-name: blackcurrant as food
-synonym: "blackcurrant" EXACT [TyDI:54518]
-is_a: OBT:001904 ! blackcurrant and primary derivative thereof
-
-[Term]
-id: OBT:002369
-name: blueberry as food
-synonym: "blueberry" EXACT [TyDI:51062]
-is_a: OBT:001907 ! blueberry and primary derivative thereof
-
-[Term]
-id: OBT:002370
-name: bonito meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002371
-name: brackish water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002372
-name: brewery
-is_a: OBT:002039 ! food fermentation factory
-
-[Term]
-id: OBT:002373
-name: brioche
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002374
-name: broccoli
-is_a: OBT:001915 ! broccoli and related product
-
-[Term]
-id: OBT:002375
-name: brussel sprout as food
-synonym: "brussel sprout" RELATED [TyDI:53198]
-is_a: OBT:001916 ! brussel sprout and related product
-
-[Term]
-id: OBT:002376
-name: buegill sunfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002377
-name: burnt soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002378
-name: calcareous ooze
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002379
-name: carbonated bottled water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002380
-name: cardoon
-is_a: OBT:001933 ! cardoon and related product
-
-[Term]
-id: OBT:002381
-name: carp meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002382
-name: carrot
-is_a: OBT:001934 ! carrot and related product
-
-[Term]
-id: OBT:002383
-name: catfish meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002384
-name: cauliflower as food
-is_a: OBT:001937 ! cauliflower and related product
-
-[Term]
-id: OBT:002385
-name: celeriac
-is_a: OBT:001938 ! celeriac and related product
-
-[Term]
-id: OBT:002386
-name: celery
-is_a: OBT:001939 ! celery and related product
-
-[Term]
-id: OBT:002387
-name: celery leaf
-is_a: OBT:001940 ! celery leaf and related product
-
-[Term]
-id: OBT:002388
-name: chard
-is_a: OBT:001943 ! chard and related product
-
-[Term]
-id: OBT:002389
-name: chemically stressed soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002390
-name: chemocline
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002391
-name: cherry as food
-synonym: "cherry" EXACT [TyDI:50286]
-is_a: OBT:001946 ! cherry and primary derivative thereof
-
-[Term]
-id: OBT:002392
-name: cherry tomato
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002393
-name: chhena
-synonym: "chhana" EXACT [TyDI:55480]
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002394
-name: chicken meat
-synonym: "broiler meat" RELATED [TyDI:54389]
-synonym: "chicken" RELATED [TyDI:53594]
-synonym: "retailed chicken" RELATED [TyDI:54390]
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002395
-name: chili pepper
-synonym: "chile pepper" EXACT [TyDI:50029]
-synonym: "chilli" EXACT [TyDI:50031]
-synonym: "chilli pepper" EXACT [TyDI:50030]
-is_a: OBT:001950 ! chili pepper and related product
-
-[Term]
-id: OBT:002396
-name: chimpanzee
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002397
-name: chinchilla
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002398
-name: chive
-is_a: OBT:001953 ! chive and related product
-
-[Term]
-id: OBT:002399
-name: citronella grass
-synonym: "Cymbopogon nardus" EXACT [TyDI:54096]
-is_a: OBT:001955 ! citronella grass and related product
-
-[Term]
-id: OBT:002400
-name: clove
-is_a: OBT:001957 ! clove and related product
-
-[Term]
-id: OBT:002401
-name: coarse beach sand
-is_a: OBT:001896 ! beach sand
-
-[Term]
-id: OBT:002402
-name: coastal sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002403
-name: cod meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002405
-name: cold soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002407
-name: cool soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002408
-name: cottage cheese
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002409
-name: cotyledon
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002410
-name: courgette
-is_a: OBT:001972 ! courgette and related product
-
-[Term]
-id: OBT:002411
-name: crab as food
-is_a: OBT:001977 ! crab and product thereof
-
-[Term]
-id: OBT:002412
-name: cranberry as food
-is_a: OBT:001979 ! cranberry and primary derivative thereof
-
-[Term]
-id: OBT:002413
-name: cream pastry
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002414
-name: creamery
-is_a: OBT:001988 ! dairy processing plant
-
-[Term]
-id: OBT:002415
-name: creek sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002416
-name: croissant
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002417
-name: crusty bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002418
-name: cucumber
-is_a: OBT:001981 ! cucumber and related product
-
-[Term]
-id: OBT:002419
-name: date as food
-synonym: "date" EXACT [TyDI:50268]
-is_a: OBT:001989 ! date and primary derivative thereof
-
-[Term]
-id: OBT:002420
-name: deep-sea sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002421
-name: deer meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002422
-name: deer tick
-synonym: "Ixodes scapularis" EXACT [TyDI:52581]
-is_a: OBT:002072 ! hard tick
-
-[Term]
-id: OBT:002423
-name: ditch sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002424
-name: dog tick
-is_a: OBT:002072 ! hard tick
-
-[Term]
-id: OBT:002425
-name: dolphinfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002426
-name: dry soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002427
-name: duck meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002428
-name: durian as food
-synonym: "durian" EXACT [TyDI:55310]
-is_a: OBT:002010 ! durian and primary derivative thereof
-
-[Term]
-id: OBT:002429
-name: eel meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002430
-name: egg cell
-is_a: OBT:002013 ! egg sac part
-
-[Term]
-id: OBT:002431
-name: elk meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002432
-name: embryonic axis
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002433
-name: embryonic axis part
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002434
-name: emperor meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002435
-name: enriched bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002436
-name: enriched soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002437
-name: erythrocyte
-synonym: "red blood cell" EXACT [TyDI:54125]
-is_a: OBT:000061 ! cell
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:002438
-name: escarole
-is_a: OBT:002021 ! escarole and related product
-
-[Term]
-id: OBT:002439
-name: eutrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002444
-name: fennel
-is_a: OBT:002024 ! fennel and related product
-
-[Term]
-id: OBT:002445
-name: field soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002446
-name: fig as food
-synonym: "fig" EXACT [TyDI:50255]
-is_a: OBT:002027 ! fig and primary derivative thereof
-
-[Term]
-id: OBT:002447
-name: filtered tap water
-is_a: OBT:002283 ! tap water
-
-[Term]
-id: OBT:002448
-name: finch
-is_a: OBT:002172 ! passerine bird
-
-[Term]
-id: OBT:002449
-name: flavoured water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002450
-name: flouder meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002451
-name: footwarm bath
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002452
-name: forest pond sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002455
-name: freshwater
-synonym: "fresh water" EXACT [TyDI:55545]
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002456
-name: freshwater bream meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002457
-name: frog leg
-is_a: OBT:002050 ! frog product
-
-[Term]
-id: OBT:002458
-name: frozen soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002459
-name: gamefowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002460
-name: garlic as food
-is_a: OBT:002058 ! garlic and related product
-
-[Term]
-id: OBT:002461
-name: gherkin
-is_a: OBT:002060 ! gherkin and related product
-
-[Term]
-id: OBT:002462
-name: gluten-free bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002463
-name: goose meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002464
-name: grape leaf
-is_a: OBT:002067 ! grape leaf and related product
-
-[Term]
-id: OBT:002465
-name: greenhouse soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002466
-name: ground beef
-is_a: OBT:001899 ! beef
-
-[Term]
-id: OBT:002467
-name: ground water
-synonym: "groundwater" EXACT [TyDI:58276]
-synonym: "subterranean water" RELATED [TyDI:58277]
-synonym: "underground water" EXACT [TyDI:58278]
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002468
-name: groundwater body
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:002469
-name: guinea fowl meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002470
-name: guinea pig
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002471
-name: haddock meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002472
-name: hake meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002473
-name: halibut meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002474
-name: ham
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002475
-name: hamster
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002476
-name: hare meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002477
-name: head cabbage
-synonym: "cabbage" RELATED [TyDI:53192]
-is_a: OBT:002075 ! head cabbage and related product
-
-[Term]
-id: OBT:002479
-name: heat stressed soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002481
-name: herring emat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002482
-name: hilum
-is_a: OBT:002288 ! testa part
-
-[Term]
-id: OBT:002483
-name: horseradish
-is_a: OBT:002081 ! horseradish and related product
-
-[Term]
-id: OBT:002484
-name: hospital bed
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002485
-name: hospital nebulizer
-synonym: "hospital nebuliser" EXACT [TyDI:55172]
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002486
-name: hospital water supply
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002487
-name: hot tap water
-is_a: OBT:002283 ! tap water
-
-[Term]
-id: OBT:002488
-name: human
-synonym: "homo sapiens" EXACT [TyDI:52730]
-synonym: "individual" RELATED [TyDI:52728]
-synonym: "people" RELATED [TyDI:52731]
-synonym: "person" RELATED [TyDI:52727]
-synonym: "subject" EXACT [TyDI:52729]
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002489
-name: human filarial nematode
-is_a: OBT:002028 ! filarial nematode
-
-[Term]
-id: OBT:002490
-name: human louse
-synonym: "Pediculus humanus" EXACT [TyDI:54240]
-is_a: OBT:002116 ! louse
-
-[Term]
-id: OBT:002491
-name: hyper saline brine sediment
-synonym: "highly saline brine" RELATED [TyDI:54301]
-is_a: OBT:002236 ! saline brine sediment
-
-[Term]
-id: OBT:002495
-name: jacuzzi
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002496
-name: kaki as food
-synonym: "kaki" EXACT [TyDI:50258]
-is_a: OBT:002090 ! kaki and primary derivative thereof
-
-[Term]
-id: OBT:002497
-name: kangaroo
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002498
-name: kiwi as food
-synonym: "kiwi" EXACT [TyDI:50265]
-is_a: OBT:002091 ! kiwi and primary derivative thereof
-
-[Term]
-id: OBT:002499
-name: lake sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002500
-name: landfowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002501
-name: laurel
-is_a: OBT:002098 ! laurel and related product
-
-[Term]
-id: OBT:002502
-name: lavander
-synonym: "lavandula augustifolia" EXACT [TyDI:54151]
-is_a: OBT:002099 ! lavander and related product
-
-[Term]
-id: OBT:002503
-name: leavened bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002504
-name: leek
-is_a: OBT:002101 ! leek and related product
-
-[Term]
-id: OBT:002505
-name: lemon as food
-synonym: "lemon" EXACT [TyDI:50315]
-is_a: OBT:002103 ! lemon and primary derivative thereof
-
-[Term]
-id: OBT:002506
-name: lettuce
-is_a: OBT:002105 ! lettuce and related product
-
-[Term]
-id: OBT:002507
-name: lime as food
-synonym: "lime" EXACT [TyDI:50292]
-is_a: OBT:002106 ! lime and primary derivative thereof
-
-[Term]
-id: OBT:002508
-name: litchi as food
-synonym: "litchi" EXACT [TyDI:50252]
-is_a: OBT:002111 ! litchi and primary derivative thereof
-
-[Term]
-id: OBT:002509
-name: lobster as food
-is_a: OBT:002114 ! lobster and product thereof
-
-[Term]
-id: OBT:002510
-name: louse-born
-is_a: OBT:002116 ! louse
-
-[Term]
-id: OBT:002511
-name: low nutrient aquatic habitat
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002512
-name: mackerel meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002513
-name: maize
-synonym: "corn" NARROW []
-is_a: OBT:002120 ! maize and primary derivative thereof
-
-[Term]
-id: OBT:002514
-name: mandarin as food
-synonym: "mandarin" EXACT [TyDI:50309]
-is_a: OBT:002121 ! mandarin and primary derivative thereof
-
-[Term]
-id: OBT:002515
-name: mango as food
-synonym: "mango" EXACT [TyDI:50247]
-is_a: OBT:002122 ! mango and primary derivative thereof
-
-[Term]
-id: OBT:002516
-name: marine marsh sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002517
-name: marine sulfidic sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002518
-name: medical center
-is_a: OBT:000011 ! medical environment
-is_a: OBT:000963 ! welfare center
-
-[Term]
-id: OBT:002519
-name: melon as food
-is_a: OBT:002132 ! melon and related product
-
-[Term]
-id: OBT:002520
-name: mesotrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002524
-name: milk rice
-synonym: "kiribath" EXACT [TyDI:57336]
-is_a: OBT:002224 ! rice pudding
-
-[Term]
-id: OBT:002525
-name: millet
-is_a: OBT:002137 ! millet and primary derivative thereof
-
-[Term]
-id: OBT:002526
-name: mineral water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002527
-name: mink
-is_a: OBT:002148 ! mustelidae
-
-[Term]
-id: OBT:002528
-name: mint
-is_a: OBT:002138 ! mint and related product
-
-[Term]
-id: OBT:002529
-name: mullet meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002530
-name: murine
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002531
-name: mushroom bed
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002532
-name: muskrat
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002533
-name: nectarine as food
-synonym: "nectarine" EXACT [TyDI:50279]
-is_a: OBT:002150 ! nectarine and primary derivative thereof
-
-[Term]
-id: OBT:002534
-name: nitrogen-poor soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002535
-name: nutrient-poor soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002536
-name: oat as food
-is_a: OBT:002154 ! oat and primary derivative thereof
-
-[Term]
-id: OBT:002537
-name: okra
-is_a: OBT:002157 ! okra and related product
-
-[Term]
-id: OBT:002538
-name: oligotrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002539
-name: onion
-is_a: OBT:002160 ! onion and related product
-
-[Term]
-id: OBT:002540
-name: orange as food
-synonym: "orange" EXACT [TyDI:50320]
-is_a: OBT:002162 ! orange and primary derivative thereof
-
-[Term]
-id: OBT:002541
-name: oregano
-synonym: "Origanum vulgare" EXACT [TyDI:55299]
-is_a: OBT:002164 ! oregano and related product
-
-[Term]
-id: OBT:002542
-name: paddle fish meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002543
-name: palm heart
-is_a: OBT:002167 ! palm heart and related product
-
-[Term]
-id: OBT:002544
-name: parakeet
-is_a: OBT:002169 ! parrot
-
-[Term]
-id: OBT:002545
-name: parsley
-is_a: OBT:002170 ! parsley and related product
-
-[Term]
-id: OBT:002546
-name: parsnip
-is_a: OBT:002171 ! parsnip and related product
-
-[Term]
-id: OBT:002547
-name: peach as food
-synonym: "peach" EXACT [TyDI:50289]
-is_a: OBT:002176 ! peach and primary derivative thereof
-
-[Term]
-id: OBT:002548
-name: pear as food
-synonym: "pear" EXACT [TyDI:50303]
-is_a: OBT:002179 ! pear and primary derivative thereof
-
-[Term]
-id: OBT:002549
-name: pear tomato
-synonym: "corn seed" RELATED [TyDI:54233]
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002550
-name: perch meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002551
-name: permafrost
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002552
-name: pheasant meat
-is_a: OBT:002056 ! game bird meat
-
-[Term]
-id: OBT:002553
-name: photic zone
-synonym: "euphotic zone" RELATED [TyDI:54119]
-synonym: "illuminated aquatic environment" RELATED [TyDI:54120]
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002554
-name: pickles
-is_a: OBT:002184 ! pickled food
-
-[Term]
-id: OBT:002555
-name: pico de gallo
-is_a: OBT:002139 ! mixed vegetable
-
-[Term]
-id: OBT:002556
-name: pig's trotter
-synonym: "pettitoe" RELATED [TyDI:55977]
-is_a: OBT:001866 ! animal foot
-
-[Term]
-id: OBT:002557
-name: pigeon meat
-is_a: OBT:002056 ! game bird meat
-
-[Term]
-id: OBT:002558
-name: pineapple as food
-synonym: "pineapple" EXACT [TyDI:50239]
-is_a: OBT:002188 ! pineapple and primary derivative thereof
-
-[Term]
-id: OBT:002559
-name: plum tomato
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002560
-name: pork chop
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002561
-name: potato as food
-is_a: OBT:002197 ! potato and related product
-
-[Term]
-id: OBT:002562
-name: poultry deep litter
-is_a: OBT:002198 ! poultry litter
-
-[Term]
-id: OBT:002563
-name: prawn
-synonym: "shrimp" RELATED [TyDI:56014]
-is_a: OBT:002200 ! prawn and product thereof
-
-[Term]
-id: OBT:002564
-name: public sauna
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002565
-name: puff pastry
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002566
-name: pumpkin
-is_a: OBT:002205 ! pumpkin and related product
-
-[Term]
-id: OBT:002567
-name: quail meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002568
-name: quark
-synonym: "quarg" EXACT [TyDI:55435]
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002569
-name: queso blanco
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002570
-name: queso fresco
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002571
-name: quince as food
-synonym: "quince" EXACT [TyDI:50306]
-is_a: OBT:002208 ! quince and primary derivative thereof
-
-[Term]
-id: OBT:002572
-name: rabbit
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002573
-name: radish
-is_a: OBT:002215 ! radish and related product
-
-[Term]
-id: OBT:002574
-name: raspberry as food
-synonym: "raspberry" EXACT [TyDI:50787]
-is_a: OBT:002218 ! raspberry and primary derivative thereof
-
-[Term]
-id: OBT:002575
-name: rat flea
-is_a: OBT:002034 ! flea
-
-[Term]
-id: OBT:002576
-name: ratite meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002577
-name: ray meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002578
-name: redcurrant as food
-synonym: "redcurrant" EXACT [TyDI:54515]
-is_a: OBT:002220 ! redcurrant and primary derivative thereof
-
-[Term]
-id: OBT:002579
-name: rhubarb
-is_a: OBT:002222 ! rhubarb and related product
-
-[Term]
-id: OBT:002580
-name: rice
-is_a: OBT:002223 ! rice and primary derivative thereof
-
-[Term]
-id: OBT:002581
-name: rice paddy
-synonym: "rice field" RELATED [TyDI:56094]
-synonym: "rice paddies" EXACT [TyDI:56095]
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002582
-name: rice straw
-is_a: OBT:002271 ! straw
-
-[Term]
-id: OBT:002583
-name: rice waste
-is_a: OBT:002225 ! rice-plant residue
-
-[Term]
-id: OBT:002584
-name: rice-straw residue
-is_a: OBT:002225 ! rice-plant residue
-
-[Term]
-id: OBT:002585
-name: river sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002586
-name: roach meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002587
-name: rocket
-is_a: OBT:002229 ! rocket and related product
-
-[Term]
-id: OBT:002588
-name: rosemary
-is_a: OBT:002231 ! rosemary and related product
-
-[Term]
-id: OBT:002589
-name: ruminant
-synonym: "ruminant livestock" EXACT [TyDI:52724]
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002590
-name: rye
-is_a: OBT:002233 ! rye and primary derivative thereof
-
-[Term]
-id: OBT:002591
-name: sage
-is_a: OBT:002234 ! sage and related product
-
-[Term]
-id: OBT:002592
-name: saline water
-synonym: "salt water" EXACT [TyDI:58269]
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002593
-name: salmon meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002594
-name: salsify
-is_a: OBT:002237 ! salsify and related product
-
-[Term]
-id: OBT:002595
-name: salt pork
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002596
-name: sardine meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002597
-name: shad meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002598
-name: shallot
-is_a: OBT:002247 ! shallot and related product
-
-[Term]
-id: OBT:002599
-name: shark meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002600
-name: siliceous ooze
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002601
-name: smelt meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002602
-name: sole meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002603
-name: spa
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002604
-name: spinach
-is_a: OBT:002260 ! spinach and related product
-
-[Term]
-id: OBT:002605
-name: spring sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002606
-name: squirrel
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002607
-name: strawberry as food
-synonym: "strawberry" EXACT [TyDI:50300]
-is_a: OBT:002272 ! strawberry and primary derivative thereof
-
-[Term]
-id: OBT:002608
-name: stream sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002609
-name: sturgeon meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002610
-name: sugar cane field
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002611
-name: sulfide-rich freshwater sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002612
-name: sulfidic coastal sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002613
-name: surgery
-synonym: "surgical" RELATED [TyDI:50859]
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002614
-name: surgical device
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002615
-name: swede
-is_a: OBT:002278 ! swede and related product
-
-[Term]
-id: OBT:002616
-name: sweet corn
-is_a: OBT:002279 ! sweet corn and related product
-
-[Term]
-id: OBT:002617
-name: sweet pepper
-is_a: OBT:002281 ! sweet pepper and related product
-
-[Term]
-id: OBT:002618
-name: sweet potato
-is_a: OBT:002282 ! sweet potato and related product
-
-[Term]
-id: OBT:002619
-name: swimming pool
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002620
-name: table grape as food
-synonym: "grape" RELATED [TyDI:51423]
-synonym: "table grape" EXACT [TyDI:55471]
-is_a: OBT:002066 ! grape and primary derivative thereof
-
-[Term]
-id: OBT:002621
-name: tarragon
-is_a: OBT:002284 ! tarragon and related product
-
-[Term]
-id: OBT:002622
-name: teff
-is_a: OBT:002285 ! teff and primary derivative thereof
-
-[Term]
-id: OBT:002623
-name: thyme
-is_a: OBT:002291 ! thyme and related product
-
-[Term]
-id: OBT:002624
-name: tilapia meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002625
-name: tomato as food
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002626
-name: triticale
-is_a: OBT:002295 ! triticale and primary derivative thereof
-
-[Term]
-id: OBT:002627
-name: tropical soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002628
-name: trout meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002629
-name: tuna meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002630
-name: turbot meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002631
-name: turkey meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002632
-name: turnip
-is_a: OBT:002297 ! turnip and related product
-
-[Term]
-id: OBT:002633
-name: velveeta
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002634
-name: venison meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002635
-name: vole
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002636
-name: waffle mixture
-is_a: OBT:002280 ! sweet dough
-
-[Term]
-id: OBT:002637
-name: wasabi
-is_a: OBT:002304 ! wasabi and related product
-
-[Term]
-id: OBT:002638
-name: water-stressed soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002639
-name: watercress
-is_a: OBT:002305 ! watercress and related product
-
-[Term]
-id: OBT:002640
-name: waterfowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002641
-name: watermelon as food
-is_a: OBT:002306 ! watermelon and related product
-
-[Term]
-id: OBT:002642
-name: wheat field
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002643
-name: wheat product
-is_a: OBT:002309 ! wheat and primary derivative thereof
-
-[Term]
-id: OBT:002644
-name: wheat semolina
-synonym: "semolina" RELATED [TyDI:54912]
-is_a: OBT:002309 ! wheat and primary derivative thereof
-
-[Term]
-id: OBT:002645
-name: white mustard
-synonym: "Brassica hirta" EXACT [TyDI:54090]
-is_a: OBT:002310 ! white mustard and related product
-
-[Term]
-id: OBT:002646
-name: white pepper
-is_a: OBT:002182 ! pepper
-
-[Term]
-id: OBT:002647
-name: whitefish meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002648
-name: wild boar meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002649
-name: wild rabbit meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002650
-name: wine grape as food
-synonym: "wine grape" EXACT [TyDI:50297]
-is_a: OBT:002066 ! grape and primary derivative thereof
-
-[Term]
-id: OBT:002651
-name: winter savory
-synonym: "Satureja montana" EXACT [TyDI:54093]
-is_a: OBT:002312 ! winter savory and related product
-
-[Term]
-id: OBT:002652
-name: witloof
-is_a: OBT:002313 ! witloof and related product
-
-[Term]
-id: OBT:002653
-name: wolffish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002654
-name: wombat
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002655
-name: wuchang bream meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002656
-name: yam
-is_a: OBT:002317 ! yam and related product
-
-[Term]
-id: OBT:002657
-name: yeast
-is_a: OBT:000114 ! microorganism
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:002658
-name: Brugia malayi
-is_a: OBT:002489 ! human filarial nematode
-
-[Term]
-id: OBT:002670
-name: anoxic river sediment
-is_a: OBT:002585 ! river sediment
-
-[Term]
-id: OBT:002686
-name: aquatic plant
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:002687
-name: aquifer
-is_a: OBT:002468 ! groundwater body
-
-[Term]
-id: OBT:002688
-name: bone marrow
-is_a: OBT:000334 ! lymphatic system part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:002689
-name: brain
-is_a: OBT:000357 ! nervous system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002690
-name: bread wheat product
-synonym: "common wheat" EXACT [TyDI:51258]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002691
-name: brine pool
-is_a: OBT:002371 ! brackish water
-
-[Term]
-id: OBT:002692
-name: broiler meat strip
-is_a: OBT:002394 ! chicken meat
-
-[Term]
-id: OBT:002693
-name: brown dog tick
-synonym: "Rhipicephalus sanguineus" EXACT [TyDI:53820]
-is_a: OBT:002424 ! dog tick
-
-[Term]
-id: OBT:002694
-name: clinic
-synonym: "clinical center" EXACT [TyDI:52715]
-is_a: OBT:002518 ! medical center
-
-[Term]
-id: OBT:002695
-name: coal mine lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002696
-name: cold-seep sediment
-is_a: OBT:002420 ! deep-sea sediment
-
-[Term]
-id: OBT:002697
-name: community
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002698
-name: cruise ship passenger
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002699
-name: cultivated plant
-is_a: OBT:000035 ! agricultural species
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:002700
-name: deer herd meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002701
-name: durum wheat product
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002702
-name: einkorn wheat product
-synonym: "einkorn" EXACT [TyDI:51248]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002703
-name: embryonic root
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002704
-name: embryonic root part
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002705
-name: emmer wheat product
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002706
-name: estuarine sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002707
-name: faucet handle
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:002708
-name: fracture water
-is_a: OBT:002467 ! ground water
-
-[Term]
-id: OBT:002709
-name: glacier
-is_a: OBT:000238 ! cold temperature environment
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:002710
-name: graft recipient
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002712
-name: healthy person
-synonym: "healthy human" RELATED [TyDI:53840]
-synonym: "healthy individual" RELATED [TyDI:53841]
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002713
-name: heart
-is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002714
-name: hospital
-synonym: "hospital environment" RELATED [TyDI:52520]
-is_a: OBT:002518 ! medical center
-
-[Term]
-id: OBT:002715
-name: hospital water distribution system
-is_a: OBT:002486 ! hospital water supply
-
-[Term]
-id: OBT:002716
-name: human body louse
-is_a: OBT:002490 ! human louse
-
-[Term]
-id: OBT:002717
-name: human head louse
-is_a: OBT:002490 ! human louse
-
-[Term]
-id: OBT:002718
-name: hydrothermal vent
-synonym: "hydrothermal vent system" RELATED [TyDI:57847]
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002719
-name: hydrothermal vent chimney
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002720
-name: hypersaline water
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:002721
-name: hypocotyl
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002722
-name: intertidal sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002723
-name: khorasan product
-synonym: "oriental wheat" RELATED [TyDI:51251]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002724
-name: kidney
-is_a: OBT:000364 ! organ
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:002725
-name: liver
-is_a: OBT:000258 ! digestive system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002726
-name: livestock
-synonym: "farm animal" RELATED [TyDI:54357]
-is_a: OBT:000035 ! agricultural species
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:002727
-name: mouse
-synonym: "mice" EXACT [TyDI:52338]
-is_a: OBT:002530 ! murine
-
-[Term]
-id: OBT:002728
-name: muskmelon
-is_a: OBT:002519 ! melon as food
-
-[Term]
-id: OBT:002729
-name: nugget
-is_a: OBT:002394 ! chicken meat
-
-[Term]
-id: OBT:002730
-name: ocean trench
-is_a: OBT:000307 ! high pressure environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002731
-name: ostrich meat
-is_a: OBT:002576 ! ratite meat
-
-[Term]
-id: OBT:002735
-name: rainwater
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:002736
-name: rat
-is_a: OBT:002530 ! murine
-
-[Term]
-id: OBT:002737
-name: red deer meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002738
-name: roe deer meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002739
-name: sake brewery
-is_a: OBT:002372 ! brewery
-
-[Term]
-id: OBT:002740
-name: salted lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002741
-name: shoot apex
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002742
-name: skin lesion
-synonym: "break in the skin" RELATED [TyDI:52525]
-is_a: OBT:000332 ! lesion
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:002743
-name: small ruminant
-is_a: OBT:002589 ! ruminant
-
-[Term]
-id: OBT:002744
-name: soda lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002745
-name: sourdough bread
-is_a: OBT:002503 ! leavened bread
-
-[Term]
-id: OBT:002746
-name: spelt product
-synonym: "dinkel wheat" EXACT [TyDI:51245]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002747
-name: stormwater
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:002748
-name: theatre shoe
-synonym: "theatre boot" EXACT [TyDI:52073]
-is_a: OBT:000341 ! medical outfit
-is_a: OBT:000420 ! shoe
-
-[Term]
-id: OBT:002749
-name: tidal flat sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002750
-name: vegetarian
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002751
-name: vinegar factory
-is_a: OBT:002372 ! brewery
-
-[Term]
-id: OBT:002752
-name: waste treatment equipment
-is_a: OBT:000167 ! waste treatment environment
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:002753
-name: waste treatment plant
-is_a: OBT:000167 ! waste treatment environment
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:002754
-name: waste water
-synonym: "wastewater" EXACT [TyDI:58161]
-is_a: OBT:000325 ! industrial water and effluent
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:002755
-name: whirlpool spa
-is_a: OBT:002603 ! spa
-
-[Term]
-id: OBT:002756
-name: yeast bread
-is_a: OBT:002503 ! leavened bread
-
-[Term]
-id: OBT:002757
-name: activated carbon filter
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002758
-name: algae
-is_a: OBT:002686 ! aquatic plant
-
-[Term]
-id: OBT:002759
-name: alluvial gravel aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002766
-name: biofilter
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002767
-name: black smoker
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002768
-name: black smoker chimney
-is_a: OBT:002719 ! hydrothermal vent chimney
-
-[Term]
-id: OBT:002769
-name: brine
-is_a: OBT:002691 ! brine pool
-
-[Term]
-id: OBT:002770
-name: cantaloupe as food
-synonym: "mushmelon" RELATED [TyDI:53523]
-synonym: "rockmelon" RELATED [TyDI:53524]
-synonym: "spanspek" RELATED [TyDI:53525]
-synonym: "sweet melon" RELATED [TyDI:53526]
-is_a: OBT:002728 ! muskmelon
-
-[Term]
-id: OBT:002771
-name: cereal crop
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002776
-name: coastal aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002777
-name: coffee plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002778
-name: contaminated sediment
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:002779
-name: cotton plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002780
-name: cultivated Leguminosae
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002781
-name: decantation tank
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002782
-name: deep-sea hot vent
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002783
-name: deep-sea hydrothermal vent
-synonym: "deep-sea hydrothermal vent site" EXACT [TyDI:49702]
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002784
-name: deep-sea hydrothermal vent chimney
-is_a: OBT:002719 ! hydrothermal vent chimney
-
-[Term]
-id: OBT:002785
-name: dendritic cell
-is_a: OBT:000320 ! immune cell
-is_a: OBT:000801 ! phagocyte
-
-[Term]
-id: OBT:002786
-name: digester
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002787
-name: dish towel
-is_a: OBT:000330 ! kitchen equipment
-is_a: OBT:000926 ! towel
-
-[Term]
-id: OBT:002788
-name: drilling bore water
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002789
-name: endothelium
-synonym: "endothelial" RELATED [TyDI:52445]
-synonym: "vascular endothelium" EXACT [TyDI:52444]
-is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:002791
-name: eschar
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:002793
-name: fish
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:002794
-name: flooded soil
-is_a: OBT:000427 ! soil
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:002795
-name: flowing water
-synonym: "running water" RELATED [TyDI:51473]
-is_a: OBT:000269 ! environment water
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:002796
-name: food processing wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002799
-name: geothermal aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002800
-name: ginseng plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002802
-name: granitic rock aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002803
-name: grapevine
-synonym: "grapewine" EXACT [TyDI:52433]
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002804
-name: home plumbing
-synonym: "home plumbing system" EXACT [TyDI:56063]
-is_a: OBT:000260 ! domestic appliance
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:002805
-name: hot water distribution system
-is_a: OBT:002715 ! hospital water distribution system
-
-[Term]
-id: OBT:002807
-name: industrial effluent treatment plant
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:002808
-name: industrial wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002810
-name: intestine
-synonym: "enteric" RELATED [TyDI:53834]
-synonym: "enteroinvasive" RELATED [TyDI:53837]
-synonym: "gut" RELATED [TyDI:51589]
-synonym: "intestinal" RELATED [TyDI:53832]
-synonym: "intestinal environment" RELATED [TyDI:53835]
-synonym: "intestinal region" RELATED [TyDI:53836]
-synonym: "intestinal tract" EXACT [TyDI:53833]
-is_a: OBT:000364 ! organ
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:002812
-name: leaching column
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002813
-name: malt vinegar brewery
-is_a: OBT:002751 ! vinegar factory
-
-[Term]
-id: OBT:002814
-name: marine microbial mat
-is_a: OBT:000338 ! marine environment
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:002815
-name: marine wetland
-is_a: OBT:000338 ! marine environment
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:002816
-name: meltwater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002828
-name: oil field water
-synonym: "oil field production water" RELATED [TyDI:53128]
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002832
-name: pharynx
-is_a: OBT:000408 ! respiratory tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:002834
-name: plant litter
-is_a: OBT:000365 ! organic matter
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:002836
-name: plumule
-is_a: OBT:002741 ! shoot apex
-
-[Term]
-id: OBT:002837
-name: probiotic feed
-synonym: "animal probiotic" EXACT []
-is_a: OBT:000038 ! animal feed
-is_a: OBT:001269 ! probiotic food
-
-[Term]
-id: OBT:002838
-name: produced water
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002841
-name: radicle
-is_a: OBT:002704 ! embryonic root part
-
-[Term]
-id: OBT:002842
-name: rennet
-is_a: OBT:000432 ! starter culture
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:002850
-name: root
-synonym: "root system" RELATED [TyDI:53850]
-is_a: OBT:000411 ! rhizosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002851
-name: saline wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002852
-name: sand aquifer
-synonym: "sandy aquifer" EXACT [TyDI:53859]
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002853
-name: scald
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:002854
-name: sewage pipe
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002855
-name: sewage plant
-synonym: "sewage treatment plant" EXACT [TyDI:51613]
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:002856
-name: shower curtain
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:000580 ! curtain
-
-[Term]
-id: OBT:002859
-name: submersed aquatic plant
-synonym: "submerged aquatic plant" EXACT [TyDI:53827]
-is_a: OBT:002686 ! aquatic plant
-
-[Term]
-id: OBT:002860
-name: sugar cane
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002862
-name: sulfate-rich wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002863
-name: sulfide mound
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:000746 ! mound
-
-[Term]
-id: OBT:002870
-name: tobacco plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002871
-name: trichome
-is_a: OBT:000054 ! biofilm
-is_a: OBT:001090 ! epidermis part
-
-[Term]
-id: OBT:002873
-name: underground mine
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:002877
-name: waste container
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002878
-name: water-table aquifer
-synonym: "drinking water aquifer" RELATED [TyDI:51841]
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002879
-name: Damselfish
-synonym: "Damselfishes" EXACT [TyDI:51336]
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002880
-name: acid mine drainage
-synonym: "AMD" EXACT [TyDI:51490]
-is_a: OBT:000176 ! acid environment
-is_a: OBT:001211 ! mine drainage
-
-[Term]
-id: OBT:002884
-name: activated carbon biofilter
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002885
-name: activated carbon fiber felt
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002889
-name: amphipod
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:002890
-name: anaerobic digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002891
-name: apron
-is_a: OBT:000330 ! kitchen equipment
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:002892
-name: barley plant
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002893
-name: brewery wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002894
-name: bryozoan
-is_a: OBT:000694 ! invertebrate species
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:002897
-name: cod
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002898
-name: compost biofilter
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002899
-name: creek water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002900
-name: drinking water treatment plant
-is_a: OBT:000597 ! drinking water facility
-is_a: OBT:000961 ! water treatment plant
-
-[Term]
-id: OBT:002901
-name: dumpster
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:002902
-name: dustbin
-synonym: "garbage can" RELATED [TyDI:52087]
-synonym: "waste bin" RELATED [TyDI:52088]
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:002903
-name: farmed fish
-synonym: "farm fish" EXACT [TyDI:51578]
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002904
-name: flower
-is_a: OBT:000494 ! anthosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002905
-name: freshwater fish
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002906
-name: fruit
-is_a: OBT:000541 ! carposphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002907
-name: gravel aquifer
-is_a: OBT:002759 ! alluvial gravel aquifer
-
-[Term]
-id: OBT:002908
-name: hagfish
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:002909
-name: heat exchanger
-is_a: OBT:000955 ! water cooling system
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:002910
-name: inorganically contaminated sediment
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002911
-name: kelp
-is_a: OBT:002758 ! algae
-
-[Term]
-id: OBT:002912
-name: leaf litter
-is_a: OBT:002834 ! plant litter
-
-[Term]
-id: OBT:002913
-name: lining of the small intestine
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000710 ! lining
-
-[Term]
-id: OBT:002914
-name: maize plant
-synonym: "corn plant" NARROW []
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002915
-name: marine and hypersaline microbial mat
-is_a: OBT:002814 ! marine microbial mat
-
-[Term]
-id: OBT:002916
-name: mill wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002917
-name: municipal sewage plant
-synonym: "communal sewage treatment plant" EXACT [TyDI:56678]
-is_a: OBT:002855 ! sewage plant
-
-[Term]
-id: OBT:002918
-name: nozzle
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:002919
-name: oat plant
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002921
-name: pericycle
-is_a: OBT:000816 ! plant tissue
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:002925
-name: pine litter
-is_a: OBT:002834 ! plant litter
-
-[Term]
-id: OBT:002926
-name: produced water from an oil well
-is_a: OBT:002838 ! produced water
-
-[Term]
-id: OBT:002927
-name: produced water of an oil reservoir
-is_a: OBT:002838 ! produced water
-
-[Term]
-id: OBT:002928
-name: pulp-bleaching waste water
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002929
-name: radioactive sediment
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002930
-name: rice plant
-synonym: "Oryza sativa" EXACT [TyDI:51517]
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002931
-name: river water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002932
-name: root nodule
-is_a: OBT:000812 ! plant nodule
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:002933
-name: salmonides
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002934
-name: seaweed
-is_a: OBT:002859 ! submersed aquatic plant
-
-[Term]
-id: OBT:002935
-name: sediment contaminated by organic pollutants
-synonym: "organically contaminated sediment" EXACT [TyDI:51598]
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002936
-name: sewage disposal plant
-is_a: OBT:002855 ! sewage plant
-
-[Term]
-id: OBT:002937
-name: shallow coastal aquifer
-is_a: OBT:002776 ! coastal aquifer
-
-[Term]
-id: OBT:002938
-name: shea cake digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002939
-name: sludge digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002940
-name: soda lake
-is_a: OBT:000187 ! alkaline environment
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:002941
-name: stem
-is_a: OBT:000545 ! caulosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002942
-name: stream water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002943
-name: tannery wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002944
-name: textile wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002946
-name: thermophilic aerobic digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002947
-name: tubeworm
-is_a: OBT:000694 ! invertebrate species
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:002948
-name: wastewater treatment digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002949
-name: water tap
-synonym: "faucet" RELATED [TyDI:57027]
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:002950
-name: wheat plant
-synonym: "wheat" RELATED [TyDI:51628]
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002951
-name: zinc- and sulfate-rich wastewater
-is_a: OBT:002862 ! sulfate-rich wastewater
-
-[Term]
-id: OBT:002952
-name: acid mine water
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:002953
-name: almond
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002954
-name: amended soil
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002956
-name: amphibian
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:002957
-name: anaerobic wastewater digester
-is_a: OBT:002948 ! wastewater treatment digester
-
-[Term]
-id: OBT:002958
-name: apple
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002960
-name: avocado
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002961
-name: banana
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002962
-name: beeswax
-is_a: OBT:000477 ! additive
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:002963
-name: berry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002964
-name: blackberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002965
-name: blueberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002966
-name: cantaloupe
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002967
-name: catfish
-is_a: OBT:002905 ! freshwater fish
-
-[Term]
-id: OBT:002968
-name: cephalopod
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001215 ! mollusc
-
-[Term]
-id: OBT:002969
-name: cherry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002970
-name: cis-dichloroethene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:002971
-name: citrus fruit
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002972
-name: coal mine lake
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:002973
-name: coconut
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002974
-name: coffee
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002976
-name: contaminated water
-synonym: "polluted water" EXACT [TyDI:51293]
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002977
-name: cotton cultivated soil
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002978
-name: drinking water system
-is_a: OBT:000597 ! drinking water facility
-is_a: OBT:001380 ! water system
-
-[Term]
-id: OBT:002979
-name: dye textile wastewater
-is_a: OBT:002944 ! textile wastewater
-
-[Term]
-id: OBT:002980
-name: edible oil and related product
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001267 ! pressed food
-
-[Term]
-id: OBT:002981
-name: egg
-is_a: OBT:000613 ! embryonic structure
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:002986
-name: grape
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002988
-name: high-level radioactive sediment
-is_a: OBT:002929 ! radioactive sediment
-
-[Term]
-id: OBT:002989
-name: hospital drinking water
-synonym: "hospital potable water" RELATED [TyDI:50807]
-is_a: OBT:000312 ! hospital water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:002990
-name: hotspring
-synonym: "hot spring" EXACT [TyDI:49581]
-is_a: OBT:000625 ! extreme high temperature environment
-is_a: OBT:001333 ! spring
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002992
-name: intestinal epithelium
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:001091 ! epithelium
-
-[Term]
-id: OBT:002993
-name: intestinal mucosa
-synonym: "gut mucosa" EXACT [TyDI:51153]
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:002994
-name: kiwi
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002995
-name: macrophage
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:002996
-name: mango
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002997
-name: marine sponge
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001332 ! sponge
-
-[Term]
-id: OBT:002998
-name: mast cell
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:002999
-name: melon
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003000
-name: moldy peanut
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003001
-name: monocyte
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:003002
-name: municipal sewage sludge digester
-is_a: OBT:002939 ! sludge digester
-
-[Term]
-id: OBT:003003
-name: naphthalene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003004
-name: neutrophil
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:003005
-name: nitrobenzene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003006
-name: oil contaminated sediment
-synonym: "petroleum contaminated sediment" EXACT [TyDI:51375]
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003007
-name: oil mill wastewater
-is_a: OBT:002916 ! mill wastewater
-
-[Term]
-id: OBT:003008
-name: olive
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003009
-name: orange
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003010
-name: papaya
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003011
-name: peach
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003012
-name: pear
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003013
-name: plant based drink
-synonym: "plant based beverage" RELATED [TyDI:53339]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:003014
-name: pleural empyema
-is_a: OBT:000818 ! pleural fluid
-is_a: OBT:001087 ! empyema
-
-[Term]
-id: OBT:003015
-name: plum
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003016
-name: propolis
-is_a: OBT:000477 ! additive
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003017
-name: pyritic acid mine drainage
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:003018
-name: raspberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003019
-name: rhizoplane
-synonym: "root epidermis" EXACT [TyDI:51430]
-is_a: OBT:000849 ! root part
-is_a: OBT:001089 ! epidermis
-
-[Term]
-id: OBT:003020
-name: root cortex
-is_a: OBT:000849 ! root part
-is_a: OBT:001050 ! cortex
-
-[Term]
-id: OBT:003021
-name: salmon
-is_a: OBT:002933 ! salmonides
-
-[Term]
-id: OBT:003022
-name: sauce
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:003023
-name: sour anaerobic digester
-is_a: OBT:002890 ! anaerobic digester
-
-[Term]
-id: OBT:003024
-name: stem nodule
-is_a: OBT:000812 ! plant nodule
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003025
-name: strawberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003026
-name: submarine hydrocarbon seep
-is_a: OBT:000338 ! marine environment
-is_a: OBT:001673 ! oil seep
-
-[Term]
-id: OBT:003027
-name: sulfide-saturated mud sediment
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:001655 ! mud sediment
-
-[Term]
-id: OBT:003029
-name: tidal marsh
-is_a: OBT:000690 ! intertidal zone
-is_a: OBT:001041 ! coastal wetland
-
-[Term]
-id: OBT:003030
-name: tomato
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003031
-name: trout
-is_a: OBT:002903 ! farmed fish
-
-[Term]
-id: OBT:003032
-name: unamended soil
-synonym: "unamended control soil" RELATED [TyDI:51282]
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:003033
-name: water pipe
-is_a: OBT:000960 ! water transport structure
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:003034
-name: acid hot spring
-synonym: "acidic hot spring" EXACT [TyDI:57379]
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003035
-name: alkaline hotspring
-synonym: "alkaline hot spring" EXACT [TyDI:54989]
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003037
-name: anoxic water
-is_a: OBT:000197 ! anoxic environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:003039
-name: bedside carafe
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003040
-name: bee pollen
-is_a: OBT:001070 ! dietary supplement
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003041
-name: boar
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003042
-name: contaminated groundwater
-is_a: OBT:002976 ! contaminated water
-
-[Term]
-id: OBT:003043
-name: contaminated soil
-synonym: "polluted soil" RELATED [TyDI:53875]
-is_a: OBT:000244 ! contaminated site
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:003044
-name: decaying plant material
-synonym: "decaying plant" RELATED [TyDI:51918]
-synonym: "decaying plant tissue" RELATED [TyDI:51917]
-is_a: OBT:001065 ! decaying matter
-is_a: OBT:001258 ! plant material
-
-[Term]
-id: OBT:003045
-name: dolphin
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003046
-name: fermented liquid
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003047
-name: fermented plant-based food
-is_a: OBT:000815 ! plant product and primary derivative thereof
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003048
-name: fox
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003049
-name: fresh meat
-is_a: OBT:001200 ! meat and meat product
-is_a: OBT:001275 ! raw meat
-
-[Term]
-id: OBT:003050
-name: freshwater hotspring
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003051
-name: freshwater marsh
-is_a: OBT:001121 ! freshwater wetland
-is_a: OBT:001198 ! marsh
-
-[Term]
-id: OBT:003052
-name: frog
-is_a: OBT:002956 ! amphibian
-
-[Term]
-id: OBT:003053
-name: goulash
-is_a: OBT:001328 ! soup
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:003054
-name: grain based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003055
-name: gum tissue
-synonym: "gingiva" EXACT [TyDI:50904]
-synonym: "gingival" RELATED [TyDI:50905]
-is_a: OBT:001217 ! mouth part
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:003056
-name: hare
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003057
-name: iguana
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003058
-name: juice
-is_a: OBT:001078 ! drink
-is_a: OBT:001267 ! pressed food
-
-[Term]
-id: OBT:003059
-name: leaf based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003060
-name: leaf epidermis
-is_a: OBT:001089 ! epidermis
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:003061
-name: legume based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003062
-name: lion
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003063
-name: neutral hotspring
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003064
-name: nut based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003065
-name: palm oil
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003066
-name: partridge
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003068
-name: pheasant
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003069
-name: pozole
-is_a: OBT:001328 ! soup
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:003070
-name: root endodermis
-is_a: OBT:001088 ! endodermis
-is_a: OBT:001287 ! root cortex part
-
-[Term]
-id: OBT:003071
-name: royal jelly
-is_a: OBT:001070 ! dietary supplement
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003072
-name: saline marsh
-synonym: "salt marsh" EXACT [TyDI:50995]
-is_a: OBT:001198 ! marsh
-is_a: OBT:001290 ! saline wetland
-
-[Term]
-id: OBT:003073
-name: seal
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003074
-name: squid
-is_a: OBT:002968 ! cephalopod
-
-[Term]
-id: OBT:003075
-name: stem cortex
-is_a: OBT:001050 ! cortex
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003076
-name: stem epidermis
-is_a: OBT:001089 ! epidermis
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003077
-name: sulfide-rich water
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:003078
-name: sunflower oil
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003079
-name: toad
-is_a: OBT:002956 ! amphibian
-
-[Term]
-id: OBT:003080
-name: Ntoba Mbodi
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003081
-name: anoxic zone of freshwater lake
-is_a: OBT:003037 ! anoxic water
-
-[Term]
-id: OBT:003082
-name: baking yeast
-synonym: "baker yeast" EXACT [TyDI:52032]
-synonym: "baker's yeast" EXACT [TyDI:52033]
-synonym: "bakery yeast" EXACT [TyDI:52031]
-is_a: OBT:000432 ! starter culture
-is_a: OBT:002657 ! yeast
-
-[Term]
-id: OBT:003083
-name: bobtail squid
-is_a: OBT:003074 ! squid
-
-[Term]
-id: OBT:003084
-name: cake
-is_a: OBT:001045 ! confectionery
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:003085
-name: carpaccio
-is_a: OBT:001275 ! raw meat
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:003086
-name: cat
-is_a: OBT:001254 ! pet
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003087
-name: cereal based drink
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003088
-name: clam juice
-is_a: OBT:003058 ! juice
-
-[Term]
-id: OBT:003089
-name: decaying fruit
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003090
-name: decaying leaf
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003091
-name: decaying wood
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003092
-name: dog
-is_a: OBT:001254 ! pet
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003093
-name: fermented dairy product
-synonym: "fermented milk product" EXACT [TyDI:51941]
-is_a: OBT:001208 ! milk and milk product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003094
-name: fermented meat
-is_a: OBT:001200 ! meat and meat product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003095
-name: fermented seafood
-is_a: OBT:001301 ! seafood and seafood product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003096
-name: fermented vegetable product
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003097
-name: garden lettuce
-synonym: "cultivated lettuce" EXACT [TyDI:52008]
-synonym: "Lactuca sativa" EXACT [TyDI:52007]
-is_a: OBT:000972 ! Asteraceae
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003098
-name: gingival margin
-is_a: OBT:003055 ! gum tissue
-
-[Term]
-id: OBT:003099
-name: humus-rich acidic ash soil
-is_a: OBT:000679 ! humus
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:003100
-name: ice cream
-is_a: OBT:001208 ! milk and milk product
-is_a: OBT:001564 ! frozen food
-
-[Term]
-id: OBT:003101
-name: illuminated anoxic zone of aquatic environment
-is_a: OBT:000197 ! anoxic environment
-is_a: OBT:002553 ! photic zone
-
-[Term]
-id: OBT:003102
-name: kebab
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:003103
-name: liver paste
-is_a: OBT:001199 ! mashed food
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:003104
-name: livestock manure
-is_a: OBT:000985 ! animal waste
-is_a: OBT:001627 ! manure
-
-[Term]
-id: OBT:003105
-name: marine water
-synonym: "ocean water" EXACT [TyDI:50869]
-synonym: "sea water" EXACT [TyDI:50870]
-synonym: "seawater" EXACT [TyDI:50868]
-is_a: OBT:000338 ! marine environment
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:003106
-name: mixed salad
-synonym: "ready-to-eat salad" RELATED [TyDI:51412]
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:003107
-name: monkey
-is_a: OBT:000967 ! wild animal
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:003108
-name: oleaginous seed based drink
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003109
-name: olive and primary derivative thereof
-is_a: OBT:001238 ! oilfruit and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:003110
-name: otter
-is_a: OBT:000967 ! wild animal
-is_a: OBT:002148 ! mustelidae
-
-[Term]
-id: OBT:003111
-name: peat
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003112
-name: pet bird
-is_a: OBT:001254 ! pet
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003113
-name: pet turtle
-is_a: OBT:001254 ! pet
-is_a: OBT:001832 ! turtle
-
-[Term]
-id: OBT:003114
-name: pizza
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:003115
-name: salt contaminated soil
-synonym: "salty soil" RELATED [TyDI:51263]
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003116
-name: septic tank
-is_a: OBT:000098 ! household good
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:003117
-name: soil contaminated with agricultural activity
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003118
-name: soil contaminated with industrial xenobiotic compound
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003119
-name: stem endodermis
-is_a: OBT:001088 ! endodermis
-is_a: OBT:001788 ! stem cortex part
-
-[Term]
-id: OBT:003120
-name: urban soil
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003121
-name: wort
-is_a: OBT:003046 ! fermented liquid
-
-[Term]
-id: OBT:003122
-name: yoghurt from bambara groundnut
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003123
-name: Euprymna scolopes
-is_a: OBT:003083 ! bobtail squid
-
-[Term]
-id: OBT:003124
-name: Gundruk
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003126
-name: arsenic contaminated-soil
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003127
-name: beer wort
-is_a: OBT:003121 ! wort
-
-[Term]
-id: OBT:003128
-name: canned olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003129
-name: cattle waste
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003130
-name: chicken manure
-synonym: "chicken waste" RELATED [TyDI:51897]
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003131
-name: choux pastry
-is_a: OBT:001045 ! confectionery
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:003132
-name: coastal water
-synonym: "coastal" RELATED [TyDI:52037]
-synonym: "coastal seawater" EXACT [TyDI:52036]
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003133
-name: coral reef water
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003134
-name: cupcake
-is_a: OBT:003084 ! cake
-
-[Term]
-id: OBT:003135
-name: custard cake
-is_a: OBT:003084 ! cake
-
-[Term]
-id: OBT:003136
-name: decaying apple
-is_a: OBT:003089 ! decaying fruit
-
-[Term]
-id: OBT:003137
-name: decaying bamboo leaf
-is_a: OBT:003090 ! decaying leaf
-
-[Term]
-id: OBT:003138
-name: decaying bark
-is_a: OBT:003091 ! decaying wood
-
-[Term]
-id: OBT:003139
-name: donkey
-is_a: OBT:001384 ! working animal
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:003140
-name: emesis basin
-synonym: "kidney dish" RELATED [TyDI:52084]
-is_a: OBT:000108 ! medical equipment
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:003141
-name: farmyard manure
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003142
-name: fermented beet
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003143
-name: fermented butter
-synonym: "beurre" EXACT [TyDI:53955]
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003144
-name: fermented cereal-based product
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003145
-name: fermented fish product
-is_a: OBT:001546 ! fermented food
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:003146
-name: fermented milk
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003147
-name: fermented shrimp paste
-is_a: OBT:003095 ! fermented seafood
-
-[Term]
-id: OBT:003148
-name: fertilized soil
-is_a: OBT:003117 ! soil contaminated with agricultural activity
-
-[Term]
-id: OBT:003149
-name: fish roe and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-is_a: OBT:001872 ! animal roe
-
-[Term]
-id: OBT:003150
-name: fish waste
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003151
-name: garlic plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003152
-name: gelato
-is_a: OBT:003100 ! ice cream
-
-[Term]
-id: OBT:003153
-name: granita
-is_a: OBT:001564 ! frozen food
-is_a: OBT:001842 ! water based dish
-
-[Term]
-id: OBT:003154
-name: horse manure
-synonym: "horse waste" RELATED [TyDI:51713]
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003155
-name: hospital humidifier
-is_a: OBT:001153 ! humidifier
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:003156
-name: ill person
-is_a: OBT:000491 ! animal with disease
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003157
-name: metal contaminated soil
-synonym: "metal-stressed soil" RELATED [TyDI:52335]
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003158
-name: olive as food
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003159
-name: onion plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003160
-name: pesticide enriched soil
-is_a: OBT:003117 ! soil contaminated with agricultural activity
-
-[Term]
-id: OBT:003161
-name: pig manure
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003162
-name: roadside soil
-is_a: OBT:003120 ! urban soil
-
-[Term]
-id: OBT:003163
-name: salt stressed soil
-is_a: OBT:003115 ! salt contaminated soil
-
-[Term]
-id: OBT:003164
-name: saltern
-is_a: OBT:000050 ! artificial water environment
-is_a: OBT:000667 ! high salt concentration environment
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:003165
-name: sauerkraut
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003166
-name: sorbet
-is_a: OBT:001564 ! frozen food
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:003167
-name: stratified marine water column
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003168
-name: submarine
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003169
-name: submarinegroundwater discharge
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003170
-name: sugar-beet refinery
-is_a: OBT:001281 ! refinery
-is_a: OBT:002275 ! sugar factory
-
-[Term]
-id: OBT:003171
-name: sushi
-is_a: OBT:001548 ! fish based dish
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:003172
-name: table olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003173
-name: tsetse fly
-synonym: "tsetse" EXACT [TyDI:52216]
-synonym: "tsetse host" RELATED [TyDI:52215]
-is_a: OBT:001453 ! blood-feeding insect
-is_a: OBT:001553 ! fly
-
-[Term]
-id: OBT:003174
-name: wastewater treatment equipment
-is_a: OBT:000201 ! artificial water structure
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:003175
-name: young adult
-is_a: OBT:001395 ! adult animal
-is_a: OBT:001849 ! young animal
-
-[Term]
-id: OBT:003176
-name: Cu-stressed soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003177
-name: Glossina
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003178
-name: acidified beer wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003179
-name: adolescent
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003180
-name: adult tsetse fly
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003181
-name: amasi
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003184
-name: baby
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003185
-name: cheesecake
-is_a: OBT:003135 ! custard cake
-
-[Term]
-id: OBT:003186
-name: chicken faeces
-is_a: OBT:003130 ! chicken manure
-
-[Term]
-id: OBT:003187
-name: chicken yard waste
-is_a: OBT:003130 ! chicken manure
-
-[Term]
-id: OBT:003188
-name: child
-synonym: "children" EXACT [TyDI:52112]
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003189
-name: chromate contaminated soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003190
-name: cinnamon
-synonym: " Cinnamomum aromaticum" EXACT [TyDI:54701]
-is_a: OBT:001784 ! spice
-is_a: OBT:001954 ! cinnamon and related product
-
-[Term]
-id: OBT:003191
-name: cod roe
-synonym: "cod egg" RELATED [TyDI:53412]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003192
-name: constructed wetland
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003193
-name: dadih
-synonym: "dadiah" EXACT [TyDI:53365]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003194
-name: dahi
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003195
-name: dry sausage
-is_a: OBT:001758 ! sausage
-is_a: OBT:002002 ! dried animal product
-
-[Term]
-id: OBT:003196
-name: female tsetse fly
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003197
-name: filmjölk
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003198
-name: fjord water
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003199
-name: flatfish-Sikhae
-is_a: OBT:003145 ! fermented fish product
-
-[Term]
-id: OBT:003200
-name: freshwater lake
-is_a: OBT:001171 ! lake
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:003201
-name: ginger
-is_a: OBT:001784 ! spice
-is_a: OBT:002061 ! ginger and related product
-
-[Term]
-id: OBT:003202
-name: glassy rim of the pillow basalt
-is_a: OBT:001583 ! glassy rind of lava
-is_a: OBT:002274 ! submarine glassy basalt
-
-[Term]
-id: OBT:003203
-name: heavy metal contaminated soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003204
-name: herbicide enriched soil
-is_a: OBT:003160 ! pesticide enriched soil
-
-[Term]
-id: OBT:003205
-name: hopped wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003206
-name: immunodeficient person
-synonym: "compromised host" EXACT [TyDI:52133]
-synonym: "compromised patient" EXACT [TyDI:52131]
-synonym: "immune-compromised patient" EXACT [TyDI:52134]
-synonym: "immune-compromised person" EXACT [TyDI:52132]
-synonym: "immunocompromised host" EXACT [TyDI:52137]
-synonym: "immunodeppressed subject" EXACT [TyDI:52136]
-synonym: "immunodepressed person" EXACT [TyDI:52135]
-is_a: OBT:003156 ! ill person
-
-[Term]
-id: OBT:003207
-name: insecticide enriched soil
-is_a: OBT:003160 ! pesticide enriched soil
-
-[Term]
-id: OBT:003208
-name: kazunoko
-synonym: "herring egg" RELATED [TyDI:53407]
-synonym: "herring roe" RELATED [TyDI:53406]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003209
-name: kefir
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003210
-name: kumis
-synonym: "koumiss" EXACT [TyDI:53355]
-synonym: "kumiss" EXACT [TyDI:53356]
-synonym: "kumys" EXACT [TyDI:53354]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003211
-name: laboratory mice
-is_a: OBT:000700 ! laboratory animal
-is_a: OBT:002727 ! mouse
-
-[Term]
-id: OBT:003212
-name: laboratory rat
-is_a: OBT:000700 ! laboratory animal
-is_a: OBT:002736 ! rat
-
-[Term]
-id: OBT:003213
-name: lagoon
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003214
-name: långfil
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003215
-name: malt
-synonym: "malted barley" EXACT [TyDI:51069]
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-is_a: OBT:002007 ! dried plant product
-
-[Term]
-id: OBT:003216
-name: masago
-synonym: "smelt egg" RELATED [TyDI:53399]
-synonym: "smelt roe" RELATED [TyDI:53398]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003217
-name: matsoni
-synonym: " Caspian Sea yoghurt" EXACT [TyDI:53361]
-synonym: "matzoon" EXACT [TyDI:53362]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003218
-name: munkoyo
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003219
-name: pantothenate enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003220
-name: patient
-synonym: "person with treated disease" RELATED [TyDI:52061]
-synonym: "treated patient" EXACT [TyDI:52062]
-is_a: OBT:003156 ! ill person
-
-[Term]
-id: OBT:003221
-name: peritrophic membrane
-is_a: OBT:000200 ! arthropod part
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:003222
-name: pet rabbit
-is_a: OBT:001254 ! pet
-is_a: OBT:002572 ! rabbit
-
-[Term]
-id: OBT:003223
-name: plum as food
-synonym: "plum" EXACT [TyDI:50276]
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-is_a: OBT:002191 ! plum and primary derivative thereof
-
-[Term]
-id: OBT:003224
-name: puparia
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003225
-name: salicylate enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003226
-name: saline lake
-is_a: OBT:001171 ! lake
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:003227
-name: saltern crystallizer pond
-is_a: OBT:003164 ! saltern
-
-[Term]
-id: OBT:003228
-name: sandwich bread
-synonym: "pan bread" RELATED [TyDI:55070]
-is_a: OBT:001436 ! bakery product
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:003229
-name: shower head
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:003230
-name: skin abscess
-is_a: OBT:000476 ! abscess
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:003231
-name: skin wound
-is_a: OBT:000970 ! wound
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:003232
-name: soil of roadside tree
-is_a: OBT:003162 ! roadside soil
-
-[Term]
-id: OBT:003233
-name: solar saltern
-is_a: OBT:003164 ! saltern
-
-[Term]
-id: OBT:003234
-name: sour milk
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003235
-name: tobiko
-synonym: "flying fish egg" RELATED [TyDI:53417]
-synonym: "flying fish roe" RELATED [TyDI:53418]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003236
-name: unhopped wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003237
-name: urea enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003238
-name: viili
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003239
-name: wastewater treatment plant
-synonym: "waste water treatment plant" EXACT [TyDI:50814]
-is_a: OBT:000961 ! water treatment plant
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:003240
-name: xueo
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003241
-name: yogurt
-synonym: "yoghourt" EXACT [TyDI:51972]
-synonym: "yoghurt" EXACT [TyDI:51971]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003242
-name: éclair
-is_a: OBT:003135 ! custard cake
-
-[Term]
-id: OBT:003243
-name: Bulgarian yogurt
-is_a: OBT:003241 ! yogurt
-
-[Term]
-id: OBT:003244
-name: Morcela de Arroz
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003245
-name: adult human
-is_a: OBT:001395 ! adult animal
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003246
-name: agricultural wastewater treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003247
-name: bite
-is_a: OBT:003231 ! skin wound
-
-[Term]
-id: OBT:003248
-name: boy
-is_a: OBT:003188 ! child
-
-[Term]
-id: OBT:003249
-name: brown mushroom
-synonym: "baby bella" EXACT [TyDI:54258]
-synonym: "brown cap mushroom" EXACT [TyDI:54259]
-synonym: "chestnut mushroom" EXACT [TyDI:54254]
-synonym: "cremini" EXACT [TyDI:54255]
-synonym: "crimini mushroom" EXACT [TyDI:54253]
-synonym: "Italian brown" EXACT [TyDI:54261]
-synonym: "Italian mushroom" EXACT [TyDI:54256]
-synonym: "Roman brown mushroom" EXACT [TyDI:54260]
-synonym: "Swiss brown mushroom" EXACT [TyDI:54257]
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003250
-name: cep
-is_a: OBT:001941 ! cep and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003251
-name: cheese factory
-is_a: OBT:001988 ! dairy processing plant
-is_a: OBT:002039 ! food fermentation factory
-
-[Term]
-id: OBT:003252
-name: chloropicrine-enriched soil
-is_a: OBT:003204 ! herbicide enriched soil
-
-[Term]
-id: OBT:003253
-name: chorizo
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003254
-name: common mushroom
-synonym: "button mushroom" EXACT [TyDI:54266]
-synonym: "champignon mushroom" EXACT [TyDI:54264]
-synonym: "cultivated mushroom" EXACT [TyDI:54267]
-synonym: "table mushroom" EXACT [TyDI:54265]
-synonym: "white mushroom" EXACT [TyDI:54268]
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003255
-name: cultivated crucifer
-is_a: OBT:001057 ! crucifer
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:003256
-name: digestive chamber
-is_a: OBT:000641 ! gastrointestinal tract
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003257
-name: domestic wastewater treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003258
-name: furuncle
-synonym: "boil" RELATED [TyDI:52122]
-is_a: OBT:003230 ! skin abscess
-
-[Term]
-id: OBT:003259
-name: girl
-is_a: OBT:003188 ! child
-
-[Term]
-id: OBT:003260
-name: highly alkaline saline soda lake
-is_a: OBT:003226 ! saline lake
-
-[Term]
-id: OBT:003261
-name: hypersaline lake
-is_a: OBT:003226 ! saline lake
-
-[Term]
-id: OBT:003262
-name: industrial waste water treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003263
-name: infant
-is_a: OBT:003184 ! baby
-
-[Term]
-id: OBT:003264
-name: marine fish
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:003265
-name: mercury-enriched soil
-is_a: OBT:003203 ! heavy metal contaminated soil
-
-[Term]
-id: OBT:003266
-name: mine waste water
-synonym: "mine wastewater" EXACT [TyDI:51583]
-synonym: "mine water" EXACT []
-is_a: OBT:001212 ! mine waste
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:003267
-name: morel
-is_a: OBT:002055 ! fungi as food
-is_a: OBT:002141 ! morel and related product
-
-[Term]
-id: OBT:003268
-name: open skin wound
-is_a: OBT:003231 ! skin wound
-
-[Term]
-id: OBT:003269
-name: patient with infectious disease
-is_a: OBT:003220 ! patient
-
-[Term]
-id: OBT:003270
-name: portobello mushroom
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003271
-name: rainwater treatment utility
-synonym: "stormwater treatment utility" EXACT [TyDI:56468]
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003272
-name: root hair
-is_a: OBT:000849 ! root part
-is_a: OBT:002871 ! trichome
-
-[Term]
-id: OBT:003273
-name: sea urchin roe
-is_a: OBT:001872 ! animal roe
-is_a: OBT:002299 ! urchin and product thereof
-
-[Term]
-id: OBT:003274
-name: submarine thermal spring
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-is_a: OBT:001820 ! thermal spring
-
-[Term]
-id: OBT:003275
-name: truffle
-is_a: OBT:002055 ! fungi as food
-is_a: OBT:002296 ! truffle and related product
-
-[Term]
-id: OBT:003276
-name: water pollution treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003277
-name: Medicago
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003278
-name: brocoli
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003279
-name: brussel sprout
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003280
-name: cabbage
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003283
-name: dairy wastewater treatment plant
-is_a: OBT:003246 ! agricultural wastewater treatment plant
-
-[Term]
-id: OBT:003284
-name: diner
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003285
-name: elderly person
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003286
-name: extreme acid mine drainage
-is_a: OBT:000626 ! extremely acid environment
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:003287
-name: fenugreek
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003288
-name: formula fed infant
-is_a: OBT:003263 ! infant
-
-[Term]
-id: OBT:003289
-name: gold mine wastewater
-is_a: OBT:003266 ! mine waste water
-
-[Term]
-id: OBT:003290
-name: guar plant
-synonym: "Cyamopsis Tetragonaloba" EXACT [TyDI:52176]
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003291
-name: inmate
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003292
-name: large intestine
-is_a: OBT:001184 ! lower gastrointestinal tract part
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003293
-name: low temperature ground water
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:002467 ! ground water
-
-[Term]
-id: OBT:003294
-name: mackerel
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003295
-name: mammalian livestock
-is_a: OBT:001625 ! mammalian
-is_a: OBT:002726 ! livestock
-
-[Term]
-id: OBT:003296
-name: mung bean plant
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003297
-name: nursing home resident
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003298
-name: pea plant
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003300
-name: poultry
-is_a: OBT:001446 ! bird
-is_a: OBT:002726 ! livestock
-
-[Term]
-id: OBT:003301
-name: ripening room
-is_a: OBT:003251 ! cheese factory
-
-[Term]
-id: OBT:003302
-name: sardine
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003303
-name: small intestine
-is_a: OBT:001366 ! upper gastrointestinal tract part
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003304
-name: soybean plant
-synonym: "Glycine hispida" EXACT [TyDI:52166]
-synonym: "Glycine max" EXACT [TyDI:52167]
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003305
-name: student
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003306
-name: tilapia
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003307
-name: tomato-marinated broiler meat strip
-is_a: OBT:001629 ! marinated food
-is_a: OBT:002692 ! broiler meat strip
-
-[Term]
-id: OBT:003308
-name: traveler
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003309
-name: tuna
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003310
-name: turbot
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003311
-name: worker
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003312
-name: Alfalfa
-synonym: "Medicago sativa" EXACT [TyDI:53729]
-is_a: OBT:003277 ! Medicago
-
-[Term]
-id: OBT:003313
-name: bus driver
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003314
-name: chicken
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003315
-name: dairy livestock
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003316
-name: duck
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003317
-name: farmer
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003318
-name: goose
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003319
-name: hen
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003320
-name: horse
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003321
-name: medical staff
-synonym: "health care worker" EXACT [TyDI:53445]
-synonym: "medical personnel" RELATED [TyDI:53447]
-synonym: "medical professional" RELATED [TyDI:53446]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003322
-name: military service member
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003323
-name: polluted seawater
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003324
-name: prostitute
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003325
-name: quail
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003327
-name: scientist
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003328
-name: slaughterer
-synonym: "slaughterman" EXACT [TyDI:53421]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003329
-name: swine
-synonym: "hog" RELATED [TyDI:53708]
-synonym: "porcine" RELATED [TyDI:53709]
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003330
-name: turkey
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003331
-name: veterinarian
-synonym: "veterinary surgeon" RELATED [TyDI:55964]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003332
-name: welder
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003333
-name: alkaline soda lake
-is_a: OBT:001399 ! alkaline lake
-is_a: OBT:002940 ! soda lake
-
-[Term]
-id: OBT:003334
-name: broiler chicken
-is_a: OBT:003314 ! chicken
-
-[Term]
-id: OBT:003335
-name: crude-oil-contaminated seawater
-is_a: OBT:003323 ! polluted seawater
-
-[Term]
-id: OBT:003336
-name: livestock boar
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003337
-name: pig
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003338
-name: researcher
-is_a: OBT:003327 ! scientist
-
-[Term]
-id: OBT:003339
-name: soldier
-is_a: OBT:003322 ! military service member
-
-[Term]
-id: OBT:003340
-name: sow
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003341
-name: ABF pig
-is_a: OBT:003337 ! pig
-
-[Term]
-id: OBT:003342
-name: bedside water bottle
-is_a: OBT:001456 ! bottle
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003343
-name: fermented beverage
-is_a: OBT:001078 ! drink
-is_a: OBT:003046 ! fermented liquid
-
-[Term]
-id: OBT:003344
-name: fermented fruit
-is_a: OBT:001122 ! fruit and primary derivative thereof
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003345
-name: organic compound contaminated soil
-synonym: "carbon source enriched soil" EXACT [TyDI:53256]
-is_a: OBT:000874 ! site contaminated with organic compound
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003346
-name: spring high in sulfide
-synonym: "sulfide-rich spring" EXACT [TyDI:53516]
-is_a: OBT:001333 ! spring
-is_a: OBT:003077 ! sulfide-rich water
-
-[Term]
-id: OBT:003347
-name: tzatziki
-is_a: OBT:000570 ! composite food
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003348
-name: PCB contaminated soil
-synonym: "soil percolated with PCP" RELATED [TyDI:53570]
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003349
-name: almond beverage
-is_a: OBT:001401 ! almond and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003350
-name: amaranth milk
-is_a: OBT:001403 ! amaranth and primary derivative thereof
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003351
-name: cashew beverage
-is_a: OBT:001475 ! cashew and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003352
-name: chili sauce
-is_a: OBT:001950 ! chili pepper and related product
-is_a: OBT:003022 ! sauce
-
-[Term]
-id: OBT:003353
-name: coconut beverage
-is_a: OBT:001495 ! coconut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003354
-name: cowpea beverage
-is_a: OBT:001696 ! pea and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003355
-name: fermented soybean
-is_a: OBT:001781 ! soybean and related product
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003356
-name: guacamole
-is_a: OBT:001887 ! avocado and primary derivative thereof
-is_a: OBT:003022 ! sauce
-
-[Term]
-id: OBT:003357
-name: hazelnut beverage
-is_a: OBT:001590 ! hazelnut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003358
-name: hospital tap water
-is_a: OBT:002283 ! tap water
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003359
-name: hydrocarbon contaminated soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003360
-name: lupin beverage
-is_a: OBT:001622 ! lupin and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003361
-name: natural gas-enriched soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003362
-name: peanut beverage
-is_a: OBT:001697 ! peanut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003363
-name: pistachio beverage
-is_a: OBT:001717 ! pistachio and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003364
-name: quinoa beverage
-is_a: OBT:001734 ! quinoa and primary derivative thereof
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003365
-name: sewerage system
-is_a: OBT:000960 ! water transport structure
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003366
-name: soy beverage
-synonym: "soy drink" EXACT []
-synonym: "soy juice" EXACT []
-synonym: "soya beverage" EXACT []
-synonym: "soya drink" EXACT []
-synonym: "soya juice" EXACT []
-is_a: OBT:001781 ! soybean and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003367
-name: sulfide-rich hot spring
-synonym: "hotspring high in sulfide" RELATED [TyDI:53332]
-is_a: OBT:003346 ! spring high in sulfide
-
-[Term]
-id: OBT:003368
-name: tea infusion
-is_a: OBT:001598 ! hot drink
-is_a: OBT:003059 ! leaf based drink
-
-[Term]
-id: OBT:003369
-name: vegetable puree
-is_a: OBT:001199 ! mashed food
-is_a: OBT:001499 ! cooked food
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:003370
-name: walnut beverage
-is_a: OBT:001838 ! walnut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003371
-name: Balinese traditional fermented sausage
-synonym: "Urutan" EXACT [TyDI:52278]
-is_a: OBT:001758 ! sausage
-is_a: OBT:003094 ! fermented meat
-
-[Term]
-id: OBT:003372
-name: PAH contaminated soil
-synonym: "polycyclic aromatic hydrocarbon contaminated soil" EXACT [TyDI:53625]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003373
-name: almond milk
-is_a: OBT:003349 ! almond beverage
-
-[Term]
-id: OBT:003374
-name: cashew milk
-synonym: "cashew juice" RELATED [TyDI:52239]
-is_a: OBT:003351 ! cashew beverage
-
-[Term]
-id: OBT:003375
-name: caviar
-synonym: "sturgeon egg" EXACT [TyDI:53427]
-synonym: "sturgeon roe" EXACT [TyDI:53426]
-is_a: OBT:001277 ! raw seafood
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003376
-name: coconut milk
-is_a: OBT:003353 ! coconut beverage
-
-[Term]
-id: OBT:003377
-name: coconut water
-synonym: "coconut juice" RELATED [TyDI:51864]
-is_a: OBT:003353 ! coconut beverage
-
-[Term]
-id: OBT:003378
-name: cowpea milk
-is_a: OBT:003354 ! cowpea beverage
-
-[Term]
-id: OBT:003379
-name: creosote contaminated soil
-synonym: "creosote-contaminated soil" EXACT [TyDI:53436]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003380
-name: deer
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-is_a: OBT:002589 ! ruminant
-
-[Term]
-id: OBT:003381
-name: fermented cheese
-is_a: OBT:001480 ! cheese
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003382
-name: flaxseed beverage
-synonym: "flax beverage" RELATED [TyDI:53535]
-is_a: OBT:001551 ! flaxseed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003383
-name: hazelnut milk
-is_a: OBT:003357 ! hazelnut beverage
-
-[Term]
-id: OBT:003384
-name: hempseed beverage
-synonym: "hemp beverage" RELATED [TyDI:53540]
-is_a: OBT:001593 ! hemp seed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003385
-name: landfill contaminated by PCB
-is_a: OBT:003348 ! PCB contaminated soil
-
-[Term]
-id: OBT:003386
-name: lupin milk
-is_a: OBT:003360 ! lupin beverage
-
-[Term]
-id: OBT:003387
-name: meju
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003388
-name: natto
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003389
-name: oil contaminated soil
-synonym: "oil impregnated soil" RELATED [TyDI:53403]
-synonym: "oil-contaminated soil" EXACT [TyDI:53402]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003390
-name: peanut milk
-is_a: OBT:003362 ! peanut beverage
-
-[Term]
-id: OBT:003391
-name: pistachio milk
-is_a: OBT:003363 ! pistachio beverage
-
-[Term]
-id: OBT:003392
-name: quinate enriched soil
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003393
-name: quinoa milk
-is_a: OBT:003364 ! quinoa beverage
-
-[Term]
-id: OBT:003394
-name: salmon egg
-synonym: "ikura" RELATED [TyDI:51548]
-synonym: "salmon roe" EXACT [TyDI:51549]
-is_a: OBT:001277 ! raw seafood
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003395
-name: sesame beverage
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003396
-name: sewer
-is_a: OBT:003365 ! sewerage system
-
-[Term]
-id: OBT:003397
-name: sour cream
-is_a: OBT:001505 ! cream
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003398
-name: sourdough
-synonym: "naturally leavened bread dough" EXACT [TyDI:54041]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003399
-name: soy milk
-synonym: "soya milk" EXACT []
-synonym: "soymilk" EXACT [TyDI:58411]
-is_a: OBT:003366 ! soy beverage
-
-[Term]
-id: OBT:003400
-name: storm drain
-synonym: " storm sewer" RELATED [TyDI:58049]
-synonym: "stormwater drain" RELATED [TyDI:58051]
-synonym: "surface water drain" RELATED [TyDI:58052]
-synonym: "surface-water drain" RELATED [TyDI:58050]
-is_a: OBT:003365 ! sewerage system
-
-[Term]
-id: OBT:003401
-name: sunflower beverage
-is_a: OBT:001805 ! sunflower seed and primary derivatives thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003402
-name: walnut milk
-is_a: OBT:003370 ! walnut beverage
-
-[Term]
-id: OBT:003403
-name: xylene contaminated soil
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003404
-name: yoghurt from fermented soybean milk
-synonym: "yoghurt from fermented soymilk" RELATED [TyDI:52603]
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003405
-name: barley beverage
-is_a: OBT:001893 ! barley and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003406
-name: brined cheese
-synonym: "pickled cheese" RELATED [TyDI:54953]
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003407
-name: chief sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003408
-name: chlorophenol-contaminated groundwater
-is_a: OBT:002467 ! ground water
-is_a: OBT:003042 ! contaminated groundwater
-
-[Term]
-id: OBT:003409
-name: contaminated soil with total petroleum hydrocarbon
-synonym: "contaminated soil with TPH" EXACT [TyDI:53454]
-is_a: OBT:003389 ! oil contaminated soil
-
-[Term]
-id: OBT:003410
-name: corn beverage
-is_a: OBT:002120 ! maize and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003411
-name: creosote wood preservative-contaminated soil
-is_a: OBT:003379 ! creosote contaminated soil
-
-[Term]
-id: OBT:003412
-name: dosa
-is_a: OBT:001744 ! rice based dish
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003413
-name: elk
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003414
-name: fermented dough
-is_a: OBT:001736 ! raw dough
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003415
-name: final sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003416
-name: flax milk
-is_a: OBT:003382 ! flaxseed beverage
-
-[Term]
-id: OBT:003417
-name: forest musk deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003418
-name: hemp milk
-is_a: OBT:003384 ! hempseed beverage
-
-[Term]
-id: OBT:003419
-name: kimchi
-is_a: OBT:002184 ! pickled food
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003420
-name: laboratory sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003421
-name: leavened dough
-is_a: OBT:001736 ! raw dough
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003422
-name: moose
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003423
-name: oat beverage
-synonym: "oat drink" EXACT []
-synonym: "oat juice" EXACT []
-synonym: "oatly drink" NARROW []
-is_a: OBT:002154 ! oat and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003424
-name: phenanthrene contaminated soil
-synonym: "phenanthrene-contaminated soil" EXACT [TyDI:53351]
-is_a: OBT:003372 ! PAH contaminated soil
-
-[Term]
-id: OBT:003425
-name: red deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003426
-name: reindeer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003427
-name: rice beverage
-synonym: "rice drink" EXACT []
-synonym: "rice juice" EXACT []
-is_a: OBT:002223 ! rice and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003428
-name: ripened cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003429
-name: sesame milk
-is_a: OBT:003395 ! sesame beverage
-
-[Term]
-id: OBT:003430
-name: soil contaminated with used engine oil
-is_a: OBT:003389 ! oil contaminated soil
-
-[Term]
-id: OBT:003431
-name: spelt beverage
-is_a: OBT:002309 ! wheat and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003432
-name: streched curd cheese
-synonym: "pasta filata" EXACT [TyDI:55043]
-synonym: "plastic curd cheese" EXACT [TyDI:55042]
-synonym: "pulled-curd cheese" EXACT [TyDI:55041]
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003433
-name: sunflower milk
-is_a: OBT:003401 ! sunflower beverage
-
-[Term]
-id: OBT:003434
-name: teff beverage
-is_a: OBT:002285 ! teff and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003435
-name: traditional sourdough
-synonym: "artisan bakery sourdough" EXACT [TyDI:51170]
-synonym: "artisanal sourdough" EXACT [TyDI:51173]
-synonym: "natural fermented sourdough" EXACT [TyDI:51174]
-synonym: "natural sourdough" EXACT [TyDI:51169]
-synonym: "naturally fermented sourdough" EXACT [TyDI:51176]
-synonym: "spontaneous sourdough" EXACT [TyDI:51171]
-synonym: "spontaneously fermented sourdough" EXACT [TyDI:51172]
-synonym: "traditionnal sourdough" EXACT [TyDI:51175]
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003436
-name: type I sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003437
-name: type II sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003438
-name: type III sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003439
-name: warm seawater
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003440
-name: whey cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003441
-name: white tail deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003442
-name: barley milk
-is_a: OBT:003405 ! barley beverage
-
-[Term]
-id: OBT:003443
-name: brocciu
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003444
-name: caciocavallo
-is_a: OBT:003432 ! streched curd cheese
-
-[Term]
-id: OBT:003446
-name: contaminated aquifer
-is_a: OBT:002687 ! aquifer
-is_a: OBT:003042 ! contaminated groundwater
-
-[Term]
-id: OBT:003447
-name: corn milk
-is_a: OBT:003410 ! corn beverage
-
-[Term]
-id: OBT:003448
-name: feta
-is_a: OBT:003406 ! brined cheese
-
-[Term]
-id: OBT:003449
-name: frozen yogurt
-is_a: OBT:001564 ! frozen food
-is_a: OBT:003241 ! yogurt
-
-[Term]
-id: OBT:003450
-name: hard cheese
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003451
-name: man
-is_a: OBT:001192 ! male animal
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003452
-name: mozzarella
-is_a: OBT:003432 ! streched curd cheese
-
-[Term]
-id: OBT:003453
-name: newborn infant
-synonym: "neonatal animal" EXACT [TyDI:53896]
-synonym: "neonate" EXACT [TyDI:53897]
-synonym: "newborn" EXACT [TyDI:53898]
-is_a: OBT:001662 ! newborn animal
-is_a: OBT:003184 ! baby
-
-[Term]
-id: OBT:003454
-name: oat milk
-synonym: "oatmilk" EXACT []
-is_a: OBT:003423 ! oat beverage
-
-[Term]
-id: OBT:003455
-name: rice milk
-synonym: "ricemilk" EXACT []
-is_a: OBT:003427 ! rice beverage
-
-[Term]
-id: OBT:003456
-name: ricotta
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003457
-name: schabziger
-synonym: "sapsago" EXACT [TyDI:55029]
-synonym: "sérac" EXACT [TyDI:55030]
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003458
-name: semi soft cheese
-synonym: "semi hard cheese" EXACT [TyDI:55022]
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003459
-name: soft cheese
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003460
-name: spelt milk
-is_a: OBT:003431 ! spelt beverage
-
-[Term]
-id: OBT:003461
-name: teff milk
-is_a: OBT:003434 ! teff beverage
-
-[Term]
-id: OBT:003462
-name: warm coastal water
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003463
-name: woman
-is_a: OBT:001103 ! female animal
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003464
-name: yeast bread dough
-is_a: OBT:003414 ! fermented dough
-
-[Term]
-id: OBT:003465
-name: Beaufort
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003466
-name: Brick cheese
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003467
-name: Caciocavallo
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003468
-name: Cantal
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003469
-name: Cheddar
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003470
-name: Comté
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003471
-name: Emmental
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003472
-name: Fontina
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003473
-name: Formaggio di Fossa
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003474
-name: Gouda
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003475
-name: Granular cheese
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003476
-name: Gruyère
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003477
-name: Laguiole
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003478
-name: Leerdammer
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003479
-name: Morbier
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003480
-name: Raclette
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003481
-name: Toma
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003482
-name: Trappist
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003483
-name: Valtellina Casera
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003484
-name: aquifer contaminated with unleaded gasoline
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003485
-name: arsenic-rich aquifer
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003486
-name: blue veined cheese
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003487
-name: cauliflower
-is_a: OBT:001391 ! Brassica
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003488
-name: chloroethene-contaminated aquifer
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003489
-name: extra hard cheese
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003490
-name: goat
-is_a: OBT:001103 ! female animal
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003491
-name: mother
-is_a: OBT:003463 ! woman
-
-[Term]
-id: OBT:003492
-name: mould ripened cheese
-is_a: OBT:003459 ! soft cheese
-
-[Term]
-id: OBT:003493
-name: pregnant woman
-is_a: OBT:003463 ! woman
-
-[Term]
-id: OBT:003494
-name: smear ripened cheese
-is_a: OBT:003459 ! soft cheese
-
-[Term]
-id: OBT:003495
-name: Asiago
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003496
-name: Bleu
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003497
-name: Blue Wensleydate
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003498
-name: Brie
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003499
-name: Buche de chèvre
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003500
-name: Camembert
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003501
-name: Carré de l'est
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003502
-name: Danablu
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003503
-name: Epoisses
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003504
-name: Gorgonzola
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003505
-name: Gubbeen
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003506
-name: Hand cheese
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003507
-name: Langres
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003508
-name: Liederkranz
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003509
-name: Limburger
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003510
-name: Livarot
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003511
-name: Maroilles
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003512
-name: Munster
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003513
-name: Neufchatel
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003514
-name: Parmesan
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003515
-name: Pont l'Evêque
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003516
-name: Reblochon
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003517
-name: Romano
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003518
-name: Roquefort
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003519
-name: Saint-Nectaire
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003520
-name: Saint-Paulin
-synonym: "Saint Paulin" EXACT [TyDI:50048]
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003521
-name: Sapsago
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003522
-name: Scimudin
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003523
-name: Spalen
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003524
-name: Stilton
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003525
-name: Taleggio
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003526
-name: Tilsit
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003527
-name: romadur
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003528
-name: working horse
-is_a: OBT:001384 ! working animal
-is_a: OBT:003320 ! horse
-
-[Term]
-id: OBT:003529
-name: decaying leaf litter
-is_a: OBT:002912 ! leaf litter
-is_a: OBT:003090 ! decaying leaf
-
-[Term]
-id: OBT:003530
-name: plant based juice
-synonym: "plant milk" RELATED [TyDI:53655]
-is_a: OBT:003013 ! plant based drink
-is_a: OBT:003058 ! juice
-
-[Term]
-id: OBT:003531
-name: sheep
-synonym: "ovin" RELATED [TyDI:54422]
-is_a: OBT:002078 ! herbivore
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003532
-name: cattle
-is_a: OBT:002589 ! ruminant
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003533
-name: fermented tea leaf
-is_a: OBT:003047 ! fermented plant-based food
-is_a: OBT:003059 ! leaf based drink
-
-[Term]
-id: OBT:003534
-name: fruit based juice
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003535
-name: garlic oil
-is_a: OBT:001044 ! condiment
-is_a: OBT:002058 ! garlic and related product
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003536
-name: olive oil
-is_a: OBT:002980 ! edible oil and related product
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003537
-name: sourdough starter
-synonym: "commercial sourdough" EXACT [TyDI:50927]
-synonym: "selected sourdough" EXACT [TyDI:50926]
-synonym: "sourdough bread starter" EXACT [TyDI:50925]
-is_a: OBT:000432 ! starter culture
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003538
-name: thyme oil
-is_a: OBT:001044 ! condiment
-is_a: OBT:002291 ! thyme and related product
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003539
-name: vegetable based juice
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003540
-name: Fuzhuan brick tea
-synonym: "Fu brick tea" EXACT [TyDI:50042]
-synonym: "Fu-zhuan brick tea" EXACT [TyDI:50043]
-is_a: OBT:003533 ! fermented tea leaf
-
-[Term]
-id: OBT:003541
-name: beer
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003542
-name: bovine
-is_a: OBT:003532 ! cattle
-
-[Term]
-id: OBT:003543
-name: cider
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003544
-name: sugar cane juice
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003545
-name: waste water pipe
-synonym: "waste pipe" RELATED [TyDI:53903]
-is_a: OBT:003033 ! water pipe
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003546
-name: wine
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003547
-name: Bristish beer
-is_a: OBT:003541 ! beer
-
-[Term]
-id: OBT:003548
-name: apple cider
-is_a: OBT:003543 ! cider
-
-[Term]
-id: OBT:003549
-name: beef cattle
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003550
-name: beer Shava
-is_a: OBT:003541 ! beer
-
-[Term]
-id: OBT:003551
-name: bison
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003552
-name: buffalo
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003553
-name: marine farm fish
-is_a: OBT:002903 ! farmed fish
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003554
-name: submarine hotspring
-is_a: OBT:002990 ! hotspring
-is_a: OBT:003274 ! submarine thermal spring
-
-[Term]
-id: OBT:003555
-name: fermented dry sausage
-is_a: OBT:003094 ! fermented meat
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003556
-name: fermented fresh cheese
-is_a: OBT:002043 ! fresh cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003557
-name: French dry sausage
-synonym: "saucisson" RELATED [TyDI:52117]
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003558
-name: Greek sausage
-synonym: "Greek salami" RELATED [TyDI:52265]
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003559
-name: cream cheese
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003560
-name: faisselle
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003561
-name: fromage blanc
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003562
-name: fuet
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003563
-name: salami
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003564
-name: petit-suisse
-is_a: OBT:003561 ! fromage blanc
-
-[Term]
-id: OBT:003565
-name: vinegar
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001044 ! condiment
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003566
-name: ewe
-is_a: OBT:001103 ! female animal
-is_a: OBT:003531 ! sheep
-
-[Term]
-id: OBT:003567
-name: malt vinegar
-synonym: "Alegar" EXACT [TyDI:53327]
-is_a: OBT:003565 ! vinegar
-
-[Term]
-id: OBT:003568
-name: rice vinegar
-is_a: OBT:003565 ! vinegar
-
-[Term]
-id: OBT:003569
-name: lamb
-is_a: OBT:001849 ! young animal
-is_a: OBT:003531 ! sheep
-
-[Term]
-id: OBT:003570
-name: soy sauce
-is_a: OBT:003022 ! sauce
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003571
-name: bull
-is_a: OBT:001192 ! male animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003572
-name: cow
-synonym: "cows" EXACT [TyDI:54619]
-is_a: OBT:001103 ! female animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003573
-name: fermented table olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-is_a: OBT:003344 ! fermented fruit
-
-[Term]
-id: OBT:003574
-name: mabisi
-is_a: OBT:003093 ! fermented dairy product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003575
-name: apple juice
-is_a: OBT:001879 ! apple and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003576
-name: beet juice
-synonym: "  beetroot juice" RELATED [TyDI:53346]
-is_a: OBT:001900 ! beetroot and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003577
-name: calf
-is_a: OBT:001849 ! young animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003578
-name: carrot juice
-is_a: OBT:001934 ! carrot and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003579
-name: celery juice
-is_a: OBT:001940 ! celery leaf and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003580
-name: chibwantu
-is_a: OBT:003144 ! fermented cereal-based product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003581
-name: cranberry juice
-is_a: OBT:001979 ! cranberry and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003582
-name: cucumber juice
-is_a: OBT:001981 ! cucumber and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003583
-name: grape juice
-is_a: OBT:002066 ! grape and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003584
-name: lemon juice
-is_a: OBT:002103 ! lemon and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003585
-name: orange juice
-is_a: OBT:002162 ! orange and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003586
-name: pineapple juice
-is_a: OBT:002188 ! pineapple and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003587
-name: tomato juice
-is_a: OBT:002293 ! tomato and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003588
-name: turnip juice
-synonym: "shalgam juice" RELATED [TyDI:51718]
-is_a: OBT:002297 ! turnip and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003589
-name: wheatgrass juice
-is_a: OBT:002309 ! wheat and primary derivative thereof
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003590
-name: acetamide enriched soil
-is_a: OBT:003204 ! herbicide enriched soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003591
-name: decaying leaf litter from a pine forest
-is_a: OBT:002925 ! pine litter
-is_a: OBT:003529 ! decaying leaf litter
-
-[Term]
-id: OBT:003592
-name: fermented cottage cheese
-is_a: OBT:002408 ! cottage cheese
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003593
-name: metata ayib
-is_a: OBT:003592 ! fermented cottage cheese
-
-[Term]
-id: OBT:003594
-name: dairy goat
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003490 ! goat
-
-[Term]
-id: OBT:003595
-name: pozol
-is_a: OBT:002120 ! maize and primary derivative thereof
-is_a: OBT:003144 ! fermented cereal-based product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003596
-name: fermented juice
-is_a: OBT:003343 ! fermented beverage
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003597
-name: fermented Elaeis Palm sap
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003598
-name: dairy sheep
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003566 ! ewe
-
-[Term]
-id: OBT:003599
-name: dairy cow
-synonym: "dairy cattle" RELATED [TyDI:54584]
-synonym: "dairy cows" EXACT [TyDI:54585]
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003572 ! cow
-
-[Term]
-id: OBT:003600
-name: fermented cabbage juice
-is_a: OBT:002075 ! head cabbage and related product
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003601
-name: tejuino
-synonym: "tejuíno" EXACT [TyDI:51685]
-is_a: OBT:003410 ! corn beverage
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003602
-name: airway epithelium
-is_a: OBT:000408 ! respiratory tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003603
-name: chicken breast meat
-is_a: OBT:002394 ! chicken meat
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003604
-name: turkey breast meat
-is_a: OBT:002631 ! turkey meat
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003605
-name: rice bran
-is_a: OBT:001458 ! bran
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003606
-name: lacrimal sac
-is_a: OBT:000277 ! eye part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003607
-name: conjunctival sac
-is_a: OBT:000277 ! eye part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003608
-name: aneurysmal sac
-synonym: "aneurysm sac" EXACT []
-synonym: "aortic sac" EXACT []
-is_a: OBT:000231 ! circulatory system part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003609
-name: abdominal air sac
-synonym: "air sac" EXACT []
-synonym: "thoracic air sac" EXACT []
-is_a: OBT:000408 ! respiratory tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003610
-name: hernial sac
-is_a: OBT:000039 ! animal part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003611
-name: umbilical cord
-is_a: OBT:000463 ! urogenital tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003612
-name: umbilical cord blood
-is_a: OBT:000521 ! blood
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003613
-name: vocal cord
-is_a: OBT:000529 ! broncho-pulmonary segment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003615
-name: box lunch
-is_a: OBT:000788 ! packed lunch
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003617
-name: environmental surface
-is_a: OBT:000006 ! artificial environment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003618
-name: ceramic tile
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003619
-name: ceramic wall tile
-is_a: OBT:003618 ! ceramic tile
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003620
-name: ceramic roofing tile
-is_a: OBT:003618 ! ceramic tile
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003621
-name: stainless steel surface
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003622
-name: PCV surface
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003623
-name: plasticized PVC
-synonym: "PVC plastic" NARROW []
-is_a: OBT:003622 ! PCV surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003624
-name: PVC film
-is_a: OBT:000787 ! packaging
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003625
-name: sealed concrete
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003626
-name: bamboo cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003627
-name: wood Cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003628
-name: plastic cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003629
-name: voice prosthesis
-is_a: OBT:003630 ! tracheoesophageal prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003630
-name: tracheoesophageal prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003631
-name: silicone rubber voice prosthesis
-is_a: OBT:003629 ! voice prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003632
-name: prosthetic cardiac device
-synonym: "intracardiac prosthesis" NARROW []
-synonym: "prosthetic cardiovascular device" NARROW []
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003633
-name: prosthetic heart valve
-synonym: "heart valve prosthesis" NARROW []
-synonym: "prosthetic valve" NARROW []
-synonym: "valvular prosthesis" NARROW []
-is_a: OBT:003632 ! prosthetic cardiac device
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003634
-name: mitral valve prosthesis
-synonym: "mitral prosthesis" EXACT []
-is_a: OBT:003633 ! prosthetic heart valve
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003635
-name: aortic prosthetic valve
-synonym: "aortic valve prosthesis" EXACT []
-synonym: "arterial prosthesis" EXACT []
-is_a: OBT:003632 ! prosthetic cardiac device
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003636
-name: orthopedic prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003637
-name: othopedic implant
-is_a: OBT:003636 ! orthopedic prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003638
-name: hip prosthesis
-synonym: "prosthetic hip joint" EXACT []
-is_a: OBT:000830 ! prosthetic joint
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003639
-name: femoral prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003640
-name: knee prosthesis
-is_a: OBT:000830 ! prosthetic joint
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003641
-name: shoulder prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003642
-name: cranial prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003643
-name: penile prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003644
-name: testicular prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003645
-name: ocular prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003646
-name: prosthetic eye
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003647
-name: iris prosthesis
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003648
-name: orbital implant
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003649
-name: cochlear implant
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003650
-name: dental implant
-is_a: OBT:000591 ! dental prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003651
-name: palatal obturator prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003652
-name: breast prosthesis
-synonym: "mammary prosthesis" EXACT []
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003653
-name: breast implant
-is_a: OBT:003652 ! breast prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003654
-name: suction-socket prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003655
-name: granular sludge
-is_a: OBT:001523 ! digester sludge
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003656
-name: aerobic granular sludge
-is_a: OBT:001861 ! anaerobic digester sludge
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003657
-name: aerobic granular sludge reactor
-synonym: "AGS reactor" EXACT []
-is_a: OBT:000180 ! aerobic bioreactor
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003658
-name: granular sludge bed reactor
-synonym: "EGSB reactor" EXACT []
-is_a: OBT:000488 ! anaerobic sludge blanket reactor
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003659
-name: public swimming bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003660
-name: indoor swimming bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003661
-name: shower bath
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003662
-name: public bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003663
-name: traditional public bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003664
-name: bath basin
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003665
-name: thermal bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003666
-name: thermal saline bath
-is_a: OBT:002592 ! saline water
-is_a: OBT:003665 ! thermal bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003667
-name: mineral bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003668
-name: spa bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003669
-name: seawater bath
-is_a: OBT:003105 ! marine water
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003670
-name: freshwater bath
-is_a: OBT:002455 ! freshwater
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003671
-name: open air bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003672
-name: spring bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003673
-name: hot water bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003674
-name: hot spring bath
-is_a: OBT:002990 ! hotspring
-is_a: OBT:003673 ! hot water bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003675
-name: hot spring spa bath
-is_a: OBT:003674 ! hot spring bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003676
-name: bath sponge
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003677
-name: bath tub heating
-is_a: OBT:000671 ! home heating system
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003678
-name: antiseptic bath
-is_a: OBT:000109 ! medical product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003679
-name: chlorhexidine bath
-is_a: OBT:003678 ! antiseptic bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003680
-name: veterinary product
-is_a: OBT:000011 ! medical environment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003681
-name: insecticide bath
-is_a: OBT:003680 ! veterinary product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003682
-name: antiseptic shower
-is_a: OBT:000109 ! medical product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003683
-name: dyeing bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003684
-name: skin tannery bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003685
-name: bleach bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003689
-name: mango tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003690
-name: lemon tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003691
-name: peach tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003692
-name: apricot tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003693
-name: quince tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003694
-name: cherry tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003695
-name: khaki tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003696
-name: lime tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003697
-name: carrot plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003698
-name: broccoli plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003699
-name: brussel sprout plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003700
-name: chinese cabbage plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003701
-name: collard green plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003702
-name: head cabbage plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003703
-name: shallot plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003704
-name: fruiting vegetable plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003705
-name: courgette plant
-synonym: "zucchini plant" EXACT []
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003706
-name: cucumber plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003707
-name: gherkin plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003708
-name: melon plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003709
-name: pumpkin plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003710
-name: sweet pepper plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003711
-name: watermelon plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003712
-name: leafy vegetable plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003713
-name: celery plant
-is_a: OBT:003712 ! leafy vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003714
-name: spinach plant
-is_a: OBT:003712 ! leafy vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003715
-name: table water
-is_a: OBT:001530 ! drinking water
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003716
-name: garment factory
-is_a: OBT:001818 ! textile mill
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003717
-name: dyeing factory
-is_a: OBT:001818 ! textile mill
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003718
-name: traditional Chinese fermented cabbage
-is_a: OBT:002321 ! Chinese cabbage
-is_a: OBT:003096 ! fermented vegetable product
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003719
-name: nasal swab
-is_a: OBT:001228 ! nasal secretion
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003720
-name: rum factory
-is_a: OBT:002039 ! food fermentation factory
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003721
-name: whisky distillery
-is_a: OBT:002039 ! food fermentation factory
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003722
-name: liquor
-is_a: OBT:001397 ! alcoholic drink
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003723
-name: udder
-is_a: OBT:000723 ! mammalian part
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003724
-name: lactic starter
-is_a: OBT:000584 ! dairy starter culture
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003726
-name: plant residue from food processing
-is_a: OBT:001558 ! food processing waste
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003727
-name: grape pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003728
-name: apple pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003729
-name: olive pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003730
-name: grape must
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003731
-name: sugarcane bagasse
-synonym: "sugar cane bagasse" EXACT []
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003732
-name: agave bagasse
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003733
-name: citrus bagasse
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003734
-name: soy bran
-is_a: OBT:000038 ! animal feed
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003735
-name: palm kernel press cake
-synonym: "residue from palm oil extraction" NARROW []
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003736
-name: sugar beet pressed pulp
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003737
-name: cranberry press cake
-is_a: OBT:001558 ! food processing waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003738
-name: forage residue
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003739
-name: cotton plant waste
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003740
-name: cottonseed hull
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003741
-name: olive press cake
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003742
-name: wood waste
-is_a: OBT:000467 ! waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003743
-name: sawdust
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003744
-name: waste house wood
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003745
-name: construction wood waste
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003746
-name: demolition wood waste
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003747
-name: hazardous industrial waste
-is_a: OBT:000685 ! industrial waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003748
-name: agricultural woody waste
-is_a: OBT:000478 ! agricultural waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003749
-name: wood waste fiber
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003750
-name: transport structure
-is_a: OBT:000162 ! transport equipment
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003751
-name: pallet
-is_a: OBT:003750 ! transport structure
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003752
-name: shipping container
-is_a: OBT:003750 ! transport structure
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003753
-name: wooden pallet
-is_a: OBT:003751 ! pallet
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003756
-name: wood barrel
-is_a: OBT:000434 ! storage equipment
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003757
-name: oak barrel
-is_a: OBT:003756 ! wood barrel
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003759
-name: bakery
-is_a: OBT:001557 ! food processing factory
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003760
-name: traditional bakery
-is_a: OBT:003759 ! bakery
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003761
-name: traditional dairy
-is_a: OBT:001988 ! dairy processing plant
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003762
-name: dairy farm
-is_a: OBT:001988 ! dairy processing plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003763
-name: snowpack
-is_a: OBT:000881 ! snow
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003764
-name: conifer needle
-is_a: OBT:000807 ! phylloplane part
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003765
-name: agricultural fence
-is_a: OBT:001183 ! livestock habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003766
-name: ungulate
-is_a: OBT:002078 ! herbivore
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003767
-name: biome type forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003768
-name: alpine forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003769
-name: tropical rain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003770
-name: arid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003771
-name: boreal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003772
-name: coastal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003773
-name: cooler rain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003774
-name: dune forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003775
-name: equatorial forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003776
-name: montane forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003777
-name: hemiboreal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003778
-name: high altitude forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003779
-name: humid lakeland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003780
-name: low mountain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003781
-name: subtropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003782
-name: taiga forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003783
-name: lowland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003784
-name: marshy forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003785
-name: mountain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003786
-name: neotropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003787
-name: paleotropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003788
-name: savannah - forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003789
-name: subalpine forest
-synonym: "sub-alpine forest" EXACT []
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003790
-name: sub-Antarctic forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003791
-name: warm sub-tropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003792
-name: dry forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003793
-name: semi - arid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003794
-name: semiarid temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003795
-name: hill forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003796
-name: hot forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003797
-name: humid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003798
-name: inland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003799
-name: moist forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003800
-name: plain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003801
-name: pluvial forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003802
-name: riverbank forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003803
-name: riverine forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003804
-name: submerged forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003805
-name: temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003806
-name: underwater forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003807
-name: upland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003808
-name: volcanic forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003809
-name: warm - temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003810
-name: wet forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003811
-name: wildland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003812
-name: drained forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003813
-name: soddy forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003814
-name: natural and managed forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003815
-name: natural forest
-is_a: OBT:003814 ! natural and managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003816
-name: virgin forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003817
-name: uncontrolled forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003818
-name: undisturbed forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003819
-name: unmanaged forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003820
-name: unpolluted forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003821
-name: preserved forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003822
-name: protected forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003823
-name: native forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003824
-name: intact forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003825
-name: primary forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003826
-name: primeval forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003827
-name: pristine area of native forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003828
-name: pristine forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003829
-name: non-burnt forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003830
-name: unburnt forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003831
-name: managed forest
-is_a: OBT:003814 ! natural and managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003832
-name: man - made forest system
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003833
-name: municipal forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003834
-name: park forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003836
-name: periurban forest
-synonym: "peri-urban" EXACT []
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003837
-name: plantation forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003838
-name: recreational forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003839
-name: reserve forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003840
-name: rural forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003841
-name: semi-natural forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003842
-name: suburban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003843
-name: urban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003844
-name: village-adjacent forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003845
-name: village forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003846
-name: wood forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003847
-name: second-growth forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003848
-name: secondary forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003849
-name: early successional forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003850
-name: burnt forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003851
-name: artificial forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003852
-name: commercial forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003853
-name: commercial plantation forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003854
-name: community forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003855
-name: disturbed forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003856
-name: disturbed urban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003857
-name: historical forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003858
-name: human disturbed forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003859
-name: old forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003860
-name: mature forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003861
-name: mature forest of high conservation value
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003862
-name: mature old-growth forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003863
-name: young forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003864
-name: forest of given species
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003865
-name: alder forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003866
-name: angiosperm-dominated forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003867
-name: arboreal forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003868
-name: argan forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003869
-name: aspen forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003870
-name: beach forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003871
-name: beech forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003872
-name: beech-dominated forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003873
-name: birch forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003874
-name: boreonemoral forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003875
-name: bosque forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003876
-name: broad-leaved forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003877
-name: broadleaf forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003878
-name: Cercocarpus forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003879
-name: chestnut forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003880
-name: cloud forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003881
-name: conifer forest
-synonym: "coniferous forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003883
-name: coppice forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003884
-name: cypress forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003885
-name: deciduous forest
-synonym: "deciduous specie forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003886
-name: deciduous dipterocarp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003888
-name: herb-rich coniferous forest
-is_a: OBT:003881 ! conifer forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003890
-name: dipterocarp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003892
-name: evergreen broad-leaved forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003893
-name: forest with dominant vegetation
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003894
-name: hardwood forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003896
-name: holm-oak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003897
-name: kelp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003898
-name: larch forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003899
-name: lucidophyllous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003900
-name: mangrove forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003901
-name: maple forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003902
-name: maso bamboo forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003903
-name: hemlock fir forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003904
-name: amabilis fir forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003906
-name: monodominant forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003907
-name: monospecific forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003908
-name: spruce forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003909
-name: Nothofagaceae forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003910
-name: Nothofagus forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003911
-name: oak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003912
-name: oak-hickory forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003914
-name: ombrophilous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003916
-name: papyrifera forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003917
-name: perennial forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003918
-name: riparian forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003919
-name: pure forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003920
-name: red pine forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003921
-name: redwood forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003922
-name: riparian woodland
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003923
-name: poplar forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003924
-name: sclerophyll forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003925
-name: seasonal dry tropical forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003926
-name: scrub forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003927
-name: semi-evergreen forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003928
-name: semideciduous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003929
-name: stone pine forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003931
-name: tanoak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003932
-name: xeric forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003933
-name: xerophytic forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003934
-name: mix forest
-synonym: "mixed forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003935
-name: papilionoid legume tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003936
-name: leguminous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003937
-name: tulip tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003938
-name: tea-oil tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003939
-name: tea plant
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003940
-name: Syzygiumcordatum tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003941
-name: shea butter tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003942
-name: rubber tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003943
-name: riparian tree specie
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003944
-name: Protea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003945
-name: Prosopis tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003946
-name: peepal tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003947
-name: Pandanus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003948
-name: pacara earpod tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003949
-name: Olea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003950
-name: Nothofagus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003951
-name: mopane tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003952
-name: Masson pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003953
-name: manuka tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003954
-name: loquat tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003955
-name: lodgepole pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003956
-name: lacquer tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003957
-name: Katsura tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003958
-name: kassod tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003959
-name: Hippophae tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003960
-name: dipterocarp tree
-synonym: "Dipterocarpaceae tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003961
-name: Dekopon tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003962
-name: cycad tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003963
-name: cupuassu tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003964
-name: cupressaceous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003965
-name: chitalpa tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003966
-name: chinquapin tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003967
-name: Casuarina tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003968
-name: Ascomycota tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003969
-name: Alnus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003970
-name: Allocasuarina tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003971
-name: South-African Protea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003972
-name: African leguminous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003973
-name: willow tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003974
-name: wild tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003976
-name: whitebark pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003977
-name: White spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003978
-name: white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003979
-name: white oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003980
-name: walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003981
-name: urban tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003982
-name: Ulmus nigra tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003983
-name: Ulmus Dodoens Elm
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003984
-name: turkey oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003985
-name: tung tree
-synonym: "tung oil tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003986
-name: tanoak tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003987
-name: Talh tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003988
-name: sycamore tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003989
-name: sweet chestnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003990
-name: Swedish spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003991
-name: sudden oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003992
-name: stone pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003993
-name: silver birch
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003994
-name: silk oak
-synonym: "silk oak tree" EXACT []
-is_a: OBT:001666 ! oak
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003995
-name: Sebertia acuminata
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003996
-name: scot pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003997
-name: riparian Alnus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003998
-name: Rhodococcus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003999
-name: redwood tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004001
-name: radiata pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004002
-name: Quercus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004003
-name: pygmy tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004004
-name: prunus tree
-synonym: "Prunus spp. tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004005
-name: poplar tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004006
-name: ponderosa pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004007
-name: pomegranate tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004008
-name: pome tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004009
-name: poison oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004010
-name: pistachio tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004011
-name: pinyon pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004012
-name: persimmon tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004013
-name: persian walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004014
-name: pepper tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004015
-name: pecan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004016
-name: Paulownia tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004017
-name: palm tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004018
-name: ornamental tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004019
-name: ornamental Prunus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004020
-name: orchard tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004021
-name: Gingko tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004022
-name: nutmeg tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004023
-name: nutgall tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004024
-name: norway spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004025
-name: North American white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004026
-name: North American oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004027
-name: needled white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004028
-name: needle pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004029
-name: Monterey pine
-synonym: "insignis pine" EXACT []
-synonym: "radiata pine" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004030
-name: Mongolian pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004031
-name: medlar tree
-synonym: "Mespilus germanica" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004032
-name: Mediterranean oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004033
-name: Maritime pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004034
-name: mangrove tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004035
-name: litchi tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004036
-name: laurel tree
-synonym: "Lauraceae tree" EXACT []
-synonym: "lauraceous tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004037
-name: Larix sibirica tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004038
-name: larch tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004039
-name: kraft pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004040
-name: Korean native pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004041
-name: Korean lacquer tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004042
-name: Korean fir tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004043
-name: Korea spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004044
-name: kiwifruit tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004045
-name: khat tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004046
-name: jujube tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004047
-name: Juglandaceae walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004048
-name: Japanese Yew tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004049
-name: Japanese larch tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004050
-name: jack pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004051
-name: Indian yew tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004052
-name: Indian oak tree
-is_a: OBT:001666 ! oak
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004053
-name: Indian cork tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004054
-name: Iberian oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004055
-name: holm oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004056
-name: Himalayan pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004057
-name: hazelnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004058
-name: guava tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004059
-name: grapefruit tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004060
-name: Garry oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004061
-name: Garcinia schomdurgkiana Pierre tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004062
-name: evergreen oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004063
-name: European white elm
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004064
-name: European hackberry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004065
-name: European elm
-is_a: OBT:001542 ! elm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004066
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004067
-name: English oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004068
-name: Engelmann spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004069
-name: Emory oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004070
-name: Eastern cottonwood tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004071
-name: Dutch elm
-is_a: OBT:001542 ! elm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004072
-name: deciduous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004073
-name: cypress tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004074
-name: cotton tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004075
-name: Azerbaijani almond tree
-is_a: OBT:001402 ! almond tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004076
-name: coffee tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004077
-name: coconut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004078
-name: cocoa tree
-synonym: "chocolate tree" EXACT []
-synonym: "Theobroma cacao" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004079
-name: clove tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004080
-name: clementine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004081
-name: chestnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004082
-name: Cherry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004083
-name: carob tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004084
-name: camellia tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004085
-name: brazil nut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004086
-name: blueberry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004087
-name: black oak tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004088
-name: Bishop pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004090
-name: Betula tree
-synonym: "Betulaceae tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004091
-name: Betula pendula tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004092
-name: beech tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004093
-name: banyan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004094
-name: avocado tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004095
-name: Austrian pine
-synonym: "Austrian pine tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004096
-name: Australian native pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004097
-name: Australian native Grey Box tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004098
-name: Australian Hibiscus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004099
-name: Aspen tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004100
-name: argan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004101
-name: Alep pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004102
-name: ald tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004103
-name: acerola tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004104
-name: acacia tree
-synonym: "acacia" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004106
-name: orchad
-is_a: OBT:000067 ! cultivated habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004107
-name: planthopper
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004108
-name: jumping plant lice
-synonym: "Psyllidae" NARROW []
-synonym: "psyllids" NARROW []
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004109
-name: sap-feeding insect
-synonym: "sap-sucking insect" NARROW []
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004110
-name: sentinel plant
-is_a: OBT:000912 ! terrestrial plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004111
-name: peony
-is_a: OBT:004110 ! sentinel plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004112
-name: piercing-sucking insect
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004113
-name: Myzus persicae
-synonym: "green peach aphid" EXACT []
-is_a: OBT:001428 ! aphid
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004114
-name: cabbage aphid
-synonym: "Brevicoryne brassicae" EXACT []
-is_a: OBT:001428 ! aphid
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004115
-name: phytophagous insect
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004116
-name: cotton boll worm
-synonym: "Helicoverpa armigera" EXACT []
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004117
-name: black cut worm
-synonym: "Agrotis ipsilon" EXACT []
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004118
-name: cotton leaf worm
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004119
-name: rice yellow stem borer
-synonym: "Scirpophaga incertulas" EXACT []
-is_a: OBT:001652 ! moth
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004120
-name: Asian citrus psyllid
-synonym: "Diaphorina citri" EXACT []
-is_a: OBT:004108 ! jumping plant lice
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004121
-name: vineyard
-is_a: OBT:000067 ! cultivated habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004122
-name: Graphocephala versuta
-is_a: OBT:002248 ! sharpshooter
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004123
-name: xylem sap-feeding insect
-is_a: OBT:004109 ! sap-feeding insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:009115
-name: palm forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-- 
GitLab


From a1a564782f6e724114c1c071c4b5b9dedeb69b78 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 12:49:22 +0000
Subject: [PATCH 62/64] Delete BioNLP-OST+EnovFood-Phenotype.obo

---
 ancillaries/BioNLP-OST+EnovFood-Phenotype.obo | 2348 -----------------
 1 file changed, 2348 deletions(-)
 delete mode 100644 ancillaries/BioNLP-OST+EnovFood-Phenotype.obo

diff --git a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo b/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
deleted file mode 100644
index 05d3f686..00000000
--- a/ancillaries/BioNLP-OST+EnovFood-Phenotype.obo
+++ /dev/null
@@ -1,2348 +0,0 @@
-format-version: 1.2
-date: 25:02:2021 17:05
-saved-by: claire
-auto-generated-by: OBO-Edit 2.3.1
-
-[Term]
-id: OBT:000002
-name: microbial phenotype
-
-[Term]
-id: OBT:000015
-name: phenotype wrt adhesion
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000016
-name: phenotype wrt community behaviour
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000017
-name: phenotype wrt environment
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000018
-name: phenotype wrt growth
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000019
-name: phenotype wrt metabolic activity
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000020
-name: phenotype wrt morphology
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000021
-name: phenotype wrt motility
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000022
-name: phenotype wrt ploidy
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000023
-name: phenotype wrt stress
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000024
-name: phenotype wrt genetic
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000025
-name: physiological phenotype
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000029
-name: adherent
-is_a: OBT:000015 ! phenotype wrt adhesion
-
-[Term]
-id: OBT:000036
-name: alloploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000037
-name: aneuploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000040
-name: anoxygenic
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000042
-name: antimicrobial activity
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000051
-name: asexual reproduction
-synonym: "asexual growth" EXACT [TyDI:50000]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000053
-name: autoploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000055
-name: bioluminescent
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000057
-name: bloom forming
-synonym: "bloom-forming" EXACT [TyDI:56194]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000060
-name: catalase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000063
-name: coagulase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000064
-name: colony morphology phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000065
-name: conjugation phenotype
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000068
-name: decarboxylase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000069
-name: diploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000070
-name: endolithic
-synonym: "endolith" EXACT [TyDI:58450]
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000072
-name: endopelic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000075
-name: endopsammic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000080
-name: epilythic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000082
-name: epipelic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000084
-name: epipsammic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000086
-name: epixylic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000096
-name: haploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000099
-name: hyphae growth
-synonym: "hyphae" EXACT [TyDI:49986]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000104
-name: lichen forming
-synonym: "lichen-forming" EXACT [TyDI:56235]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000105
-name: liquid culture morphology phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000107
-name: lytic
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000116
-name: microscopic morphological phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000117
-name: motile
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000118
-name: mutant
-is_a: OBT:000024 ! phenotype wrt genetic
-
-[Term]
-id: OBT:000120
-name: non motile
-synonym: "non-motile" EXACT [TyDI:54838]
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000122
-name: non-sporulating
-synonym: "non spore forming" RELATED [TyDI:51017]
-synonym: "non sporulating" RELATED [TyDI:51016]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000123
-name: oxidoreductase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000125
-name: phenotype wrt disease impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000126
-name: phenotype wrt energy source
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000127
-name: phenotype wrt habitat acidity
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000128
-name: phenotype wrt habitat osmolarity
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000129
-name: phenotype wrt habitat oxygen
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000130
-name: phenotype wrt habitat temperature
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000131
-name: phenotype wrt immune system impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000132
-name: phenotype wrt microbial-host interaction
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000133
-name: phenotype wrt molecule impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000134
-name: phenotype wrt nutrient abundance
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000135
-name: phenotype wrt pressure
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000136
-name: phenotype wrt radiation impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000137
-name: phenotype wrt relative humidity impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000138
-name: phenotype wrt temperature impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000139
-name: planktonic
-synonym: "free floating" EXACT [TyDI:57519]
-is_a: OBT:000015 ! phenotype wrt adhesion
-
-[Term]
-id: OBT:000142
-name: presence of nanotube
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000143
-name: presence of quorum sensing
-synonym: "quorum sensing" RELATED [TyDI:57709]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000144
-name: pseudohyphae growth
-synonym: "pseudohyphae" EXACT [TyDI:49979]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000147
-name: sexual mating
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000148
-name: sexual reproduction
-synonym: "asci formation" EXACT [TyDI:49995]
-synonym: "ascospore formation" EXACT [TyDI:49997]
-synonym: "ascus formation" EXACT [TyDI:49996]
-synonym: "meiospore formation" RELATED [TyDI:49994]
-synonym: "sexual growth" EXACT [TyDI:49993]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000150
-name: sporulating
-synonym: "endospore forming" RELATED [TyDI:57325]
-synonym: "endospore-forming" RELATED [TyDI:57324]
-synonym: "spore forming" EXACT [TyDI:57323]
-synonym: "spore liberation" EXACT [TyDI:57322]
-synonym: "spore-forming" EXACT [TyDI:57321]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000152
-name: stress resistant
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000153
-name: stress sensitive
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000154
-name: stress tolerant
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000157
-name: taxis phenotype
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000159
-name: tetraploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000163
-name: triploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000164
-name: ubiquitous
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000169
-name: wild-type
-synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotype wrt genetic
-
-[Term]
-id: OBT:000172
-name: MATa
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000173
-name: MATalpha
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000174
-name: Neisser stain phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000177
-name: acidophile
-synonym: "acidophilic " EXACT [TyDI:56123]
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000179
-name: aerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000182
-name: aerotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000183
-name: aerotolerant
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000188
-name: alkaliphile
-synonym: "alkaliphilic " EXACT [TyDI:56126]
-synonym: "alkalophile " EXACT [TyDI:56127]
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000189
-name: anaerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000192
-name: anemotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000195
-name: animal hosted
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000203
-name: auxotroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000207
-name: barotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000211
-name: bile resistant
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:000218
-name: carboxydotroph
-synonym: "carboxydotrophic " EXACT [TyDI:54401]
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000221
-name: catalase negative
-synonym: "catalase -" RELATED [TyDI:57877]
-is_a: OBT:000060 ! catalase activity
-
-[Term]
-id: OBT:000222
-name: catalase positive
-synonym: "catalase +" RELATED [TyDI:57872]
-is_a: OBT:000060 ! catalase activity
-
-[Term]
-id: OBT:000228
-name: cellular shape phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000230
-name: chemotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000235
-name: coagulase negative
-is_a: OBT:000063 ! coagulase activity
-
-[Term]
-id: OBT:000236
-name: coagulase positive
-is_a: OBT:000063 ! coagulase activity
-
-[Term]
-id: OBT:000239
-name: commensal
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000242
-name: conidial
-is_a: OBT:000150 ! sporulating
-
-[Term]
-id: OBT:000243
-name: conjugating
-is_a: OBT:000065 ! conjugation phenotype
-
-[Term]
-id: OBT:000245
-name: copiotrophic
-synonym: "copiotroph " EXACT [TyDI:54275]
-is_a: OBT:000134 ! phenotype wrt nutrient abundance
-
-[Term]
-id: OBT:000248
-name: cryophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000251
-name: decarboxylase negative
-is_a: OBT:000068 ! decarboxylase activity
-
-[Term]
-id: OBT:000252
-name: decarboxylase positive
-is_a: OBT:000068 ! decarboxylase activity
-
-[Term]
-id: OBT:000257
-name: diazotroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000262
-name: durotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000265
-name: electrotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000275
-name: extreme thermophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000276
-name: extremely acidophilic
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000278
-name: facultative aerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000279
-name: facultative anaerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000286
-name: flocculent
-synonym: "flocculant" EXACT [TyDI:57333]
-synonym: "flocculating" EXACT [TyDI:57332]
-is_a: OBT:000105 ! liquid culture morphology phenotype
-
-[Term]
-id: OBT:000288
-name: free-living
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000295
-name: gliding
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000296
-name: gram stain phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000297
-name: granular
-is_a: OBT:000105 ! liquid culture morphology phenotype
-
-[Term]
-id: OBT:000300
-name: gravitactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000304
-name: hemolytic
-synonym: "haemolytic" EXACT [TyDI:58363]
-is_a: OBT:000107 ! lytic
-
-[Term]
-id: OBT:000305
-name: heterothallic
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000310
-name: homothallic
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000317
-name: hydrotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000319
-name: hyperthermophile
-synonym: "extreme thermophile" RELATED [TyDI:56138]
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000335
-name: magnetotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000343
-name: mesophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000347
-name: microaerophile
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000353
-name: multicellular arrangement phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000359
-name: neutralophile
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000361
-name: oligotrophic
-synonym: "oligotroph " EXACT [TyDI:54278]
-is_a: OBT:000134 ! phenotype wrt nutrient abundance
-
-[Term]
-id: OBT:000367
-name: osmophile
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000368
-name: osmophobe
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000369
-name: osmotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000370
-name: osmotolerant
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000371
-name: oxidase activity
-is_a: OBT:000123 ! oxidoreductase activity
-
-[Term]
-id: OBT:000372
-name: parasite
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000375
-name: pathogen
-synonym: "infectious agent" EXACT [TyDI:54923]
-synonym: "virulence phenotype" EXACT [TyDI:54924]
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000378
-name: phenotype wrt antimicrobial impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000379
-name: phenotype wrt carbon source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000380
-name: phenotype wrt color
-is_a: OBT:000064 ! colony morphology phenotype
-
-[Term]
-id: OBT:000381
-name: phenotype wrt drug impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000382
-name: phenotype wrt habitat salinity
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000383
-name: phenotype wrt living energy source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000384
-name: phenotype wrt metal concentration impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000385
-name: phenotype wrt reducing equivalent source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000386
-name: phenotype wrt shape
-is_a: OBT:000064 ! colony morphology phenotype
-
-[Term]
-id: OBT:000387
-name: phototactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000390
-name: piezophile
-synonym: "barophile " EXACT [TyDI:54198]
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000391
-name: piezosensitive
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000392
-name: piezotolerant
-synonym: "barotolerant " EXACT [TyDI:54205]
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000394
-name: plant hosted
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000396
-name: pore forming
-is_a: OBT:000107 ! lytic
-
-[Term]
-id: OBT:000399
-name: prototroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000401
-name: psychrophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000402
-name: psychrotrophic
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000409
-name: rheotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000417
-name: sessile
-is_a: OBT:000029 ! adherent
-
-[Term]
-id: OBT:000439
-name: swarming
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000440
-name: swimming
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000441
-name: symbiont
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000443
-name: syntrophic
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000449
-name: thermophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000452
-name: thermotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000453
-name: thermotolerant
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000454
-name: thigmotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000456
-name: transconjugating
-synonym: "transconjugant" RELATED [TyDI:50685]
-is_a: OBT:000065 ! conjugation phenotype
-
-[Term]
-id: OBT:000460
-name: twitching
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000472
-name: Neisser-negative
-synonym: "Neisser -" RELATED [TyDI:57819]
-is_a: OBT:000174 ! Neisser stain phenotype
-
-[Term]
-id: OBT:000473
-name: Neisser-positive
-synonym: "Neisser +" RELATED [TyDI:57816]
-is_a: OBT:000174 ! Neisser stain phenotype
-
-[Term]
-id: OBT:000482
-name: alpha-hemolytic
-is_a: OBT:000304 ! hemolytic
-
-[Term]
-id: OBT:000499
-name: autotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000512
-name: beta-hemolytic
-is_a: OBT:000304 ! hemolytic
-
-[Term]
-id: OBT:000513
-name: big colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000517
-name: biotrophic
-synonym: "obligate biotrophic " EXACT [TyDI:55611]
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000552
-name: chained
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000555
-name: chemotroph
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000563
-name: coccobacillus
-synonym: "oval-shaped" RELATED [TyDI:57691]
-synonym: "ovoid-shaped" RELATED [TyDI:57690]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000576
-name: crabtree negative
-synonym: "crabtree-negative" EXACT [TyDI:50087]
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000577
-name: crabtree positive
-synonym: "crabtree-positive" EXACT [TyDI:50096]
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000578
-name: cuboidal
-synonym: "sarcina" RELATED [TyDI:50700]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000598
-name: drug resistant
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000599
-name: drug sensitive
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000600
-name: drug tolerant
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000609
-name: ectoparasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000614
-name: encapsulated
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000616
-name: endoparasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000617
-name: endophyte
-synonym: "endophytic " EXACT [TyDI:55602]
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000618
-name: endozootic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000620
-name: epizootic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000628
-name: filament-shaped
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000629
-name: filamentous
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000632
-name: fluffy colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000635
-name: free-living diazotroph
-is_a: OBT:000257 ! diazotroph
-
-[Term]
-id: OBT:000648
-name: gram-negative
-synonym: "gram -" RELATED [TyDI:57829]
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000649
-name: gram-positive
-synonym: "gram +" RELATED [TyDI:57824]
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000650
-name: gram-variable
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000652
-name: grape-like clustered
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000656
-name: halophile
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:000657
-name: halophobe
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:000665
-name: heterotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000712
-name: lithotroph
-is_a: OBT:000385 ! phenotype wrt reducing equivalent source
-
-[Term]
-id: OBT:000732
-name: metaphytic
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000733
-name: methanogenic
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000734
-name: methylotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000735
-name: microaerotolerant
-is_a: OBT:000183 ! aerotolerant
-
-[Term]
-id: OBT:000736
-name: microanaerobe
-is_a: OBT:000189 ! anaerobe
-
-[Term]
-id: OBT:000744
-name: mixotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000758
-name: natron-alkaliphilic
-is_a: OBT:000188 ! alkaliphile
-
-[Term]
-id: OBT:000762
-name: necrotrophic
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000763
-name: negative aerotactic
-is_a: OBT:000182 ! aerotactic
-
-[Term]
-id: OBT:000764
-name: negative chemotactic
-is_a: OBT:000230 ! chemotactic
-
-[Term]
-id: OBT:000769
-name: obligate aerobe
-is_a: OBT:000179 ! aerobe
-
-[Term]
-id: OBT:000770
-name: obligate anaerobe
-is_a: OBT:000189 ! anaerobe
-
-[Term]
-id: OBT:000771
-name: obligate parasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000772
-name: obligate piezophile
-synonym: "obligate barophile " EXACT [TyDI:54212]
-is_a: OBT:000390 ! piezophile
-
-[Term]
-id: OBT:000776
-name: opportunistic pathogen
-synonym: "opportunist" EXACT [TyDI:54918]
-is_a: OBT:000375 ! pathogen
-
-[Term]
-id: OBT:000778
-name: organotroph
-is_a: OBT:000385 ! phenotype wrt reducing equivalent source
-
-[Term]
-id: OBT:000784
-name: oxidase negative
-is_a: OBT:000371 ! oxidase activity
-
-[Term]
-id: OBT:000785
-name: oxidase positive
-is_a: OBT:000371 ! oxidase activity
-
-[Term]
-id: OBT:000789
-name: paired
-synonym: "diplobacilli" RELATED [TyDI:50739]
-synonym: "diplococci" RELATED [TyDI:50738]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000798
-name: periphytic
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000804
-name: photosynthetic
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000805
-name: phototroph
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000809
-name: pigmented
-is_a: OBT:000380 ! phenotype wrt color
-
-[Term]
-id: OBT:000813
-name: plant opportunist
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000817
-name: pleomorphic
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000821
-name: positive aerotactic
-is_a: OBT:000182 ! aerotactic
-
-[Term]
-id: OBT:000822
-name: positive chemotactic
-is_a: OBT:000230 ! chemotactic
-
-[Term]
-id: OBT:000827
-name: probiotic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000848
-name: rod-shaped
-synonym: "bacilliform" EXACT [TyDI:57694]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000850
-name: round-shaped
-synonym: "coccus" RELATED [TyDI:57763]
-synonym: "sphere-shaped" RELATED [TyDI:57762]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000865
-name: sheathed
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000872
-name: singled
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000879
-name: small colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000880
-name: smooth colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000888
-name: spiral-shaped
-synonym: "helical" RELATED [TyDI:57757]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000891
-name: square-shaped
-synonym: "cube-like-shaped" RELATED [TyDI:57732]
-synonym: "cuboidal" RELATED [TyDI:50699]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000892
-name: stalked
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000893
-name: star-shaped
-synonym: "rosette-like" RELATED [TyDI:57738]
-synonym: "star-like" RELATED [TyDI:57737]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000897
-name: structured colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000906
-name: symbiotic diazotroph
-is_a: OBT:000257 ! diazotroph
-
-[Term]
-id: OBT:000914
-name: tetrad
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000928
-name: trichome forming
-synonym: "trichome-forming" EXACT [TyDI:57617]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:001005
-name: biofilm phenotype
-is_a: OBT:000015 ! phenotype wrt adhesion
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:001007
-name: black pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001008
-name: blue pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001019
-name: brown pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001035
-name: chlorophototroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:001043
-name: comma-shaped
-synonym: "comma shaped" EXACT [TyDI:57744]
-synonym: "vibrio-shaped" RELATED [TyDI:57743]
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001054
-name: cream pigmented
-synonym: "beige pigmented" RELATED [TyDI:56779]
-synonym: "creamy white pigmented" RELATED [TyDI:56778]
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001095
-name: extreme halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001098
-name: facultative chemo lithotroph
-synonym: "facultative chemolithotroph " EXACT [TyDI:54393]
-is_a: OBT:000555 ! chemotroph
-
-[Term]
-id: OBT:001105
-name: fermentative
-synonym: "fermentation ability" EXACT [TyDI:56867]
-synonym: "fermentation capacity" EXACT [TyDI:56866]
-is_a: OBT:000665 ! heterotroph
-
-[Term]
-id: OBT:001107
-name: fluorescent pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001131
-name: golden pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001137
-name: green pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001156
-name: indigo pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001197
-name: maroon pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001203
-name: meso-halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001204
-name: methanol oxidizing
-is_a: OBT:000734 ! methylotroph
-
-[Term]
-id: OBT:001205
-name: methanotroph
-synonym: "methane-oxidizing " EXACT [TyDI:54831]
-synonym: "methanophile " EXACT [TyDI:54830]
-synonym: "methanotrophic " RELATED [TyDI:54829]
-is_a: OBT:000734 ! methylotroph
-
-[Term]
-id: OBT:001214
-name: moderate halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001233
-name: obligate halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001240
-name: orange pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001255
-name: pink pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001272
-name: purple pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001280
-name: red pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001288
-name: ropy colony
-is_a: OBT:000880 ! smooth colony
-
-[Term]
-id: OBT:001318
-name: silver pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001329
-name: spirillum
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001330
-name: spirochete
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001372
-name: violet pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001382
-name: white pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001386
-name: yellow pigmented
-synonym: "yellowish" RELATED [TyDI:57376]
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001444
-name: biofilm forming
-is_a: OBT:001005 ! biofilm phenotype
-
-[Term]
-id: OBT:001664
-name: non-biofilm forming
-is_a: OBT:001005 ! biofilm phenotype
-
-[Term]
-id: OBT:001667
-name: obligate methanotroph
-is_a: OBT:001205 ! methanotroph
-
-[Term]
-id: OBT:001712
-name: phenotype wrt chemical composition
-is_a: OBT:000023 ! phenotype wrt stress
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:001992
-name: desiccation resistant
-synonym: "dessication resistant" RELATED [TyDI:56478]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:001993
-name: desiccation sensitive
-synonym: "dessication sensitive" RELATED [TyDI:56491]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:001994
-name: desiccation tolerant
-synonym: "dessication tolerant" RELATED [TyDI:56471]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:001997
-name: disease resistant
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:001998
-name: disease sensitive
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:001999
-name: disease tolerant
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002035
-name: flor
-synonym: "flor forming" EXACT [TyDI:50074]
-is_a: OBT:001444 ! biofilm forming
-
-[Term]
-id: OBT:002183
-name: phagocytosis resistant
-is_a: OBT:000131 ! phenotype wrt immune system impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002212
-name: radiation resistant
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002213
-name: radiation sensitive
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:002214
-name: radiation tolerant
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002289
-name: thermal sensitive
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:002290
-name: thermal tolerant
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002330
-name: UV radiation resistant
-synonym: "ultraviolet resistant" EXACT [TyDI:56250]
-synonym: "UV resistant" RELATED [TyDI:56251]
-is_a: OBT:002212 ! radiation resistant
-
-[Term]
-id: OBT:002331
-name: UV radiation sensitive
-synonym: "ultraviolet sensitive" EXACT [TyDI:50769]
-synonym: "UV sensitive" EXACT [TyDI:50768]
-is_a: OBT:002213 ! radiation sensitive
-
-[Term]
-id: OBT:002332
-name: UV radiation tolerant
-synonym: "ultraviolet tolerant" EXACT [TyDI:50773]
-synonym: "UV tolerant" EXACT [TyDI:50772]
-is_a: OBT:002214 ! radiation tolerant
-
-[Term]
-id: OBT:002337
-name: antimicrobial resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002338
-name: antimicrobial sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002339
-name: antimicrobial tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002404
-name: cold sensitive
-synonym: "low temperature sensitive" RELATED [TyDI:51159]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002406
-name: cold tolerant
-synonym: "low temperature tolerant" RELATED [TyDI:51138]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002440
-name: extreme cold sensitive
-synonym: "extreme low temperature sensitive" RELATED [TyDI:51086]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002441
-name: extreme cold tolerant
-synonym: "extreme low temperature tolerant" RELATED [TyDI:51150]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002442
-name: extreme heat sensitive
-synonym: "extreme high temperature sensitive" RELATED [TyDI:51107]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002443
-name: extreme heat tolerant
-synonym: "extreme high temperature tolerant" RELATED [TyDI:51145]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002453
-name: freeze-thaw sensitive
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002454
-name: freeze-thaw tolerant
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002478
-name: heat sensitive
-synonym: "high temperature sensitive" RELATED [TyDI:50722]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002480
-name: heat tolerant
-synonym: "high temperature tolerant" RELATED [TyDI:51156]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002492
-name: ionizing radiation resistant
-is_a: OBT:002212 ! radiation resistant
-
-[Term]
-id: OBT:002493
-name: ionizing radiation sensitive
-is_a: OBT:002213 ! radiation sensitive
-
-[Term]
-id: OBT:002494
-name: ionizing radiation tolerant
-is_a: OBT:002214 ! radiation tolerant
-
-[Term]
-id: OBT:002521
-name: metal resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002522
-name: metal sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002523
-name: metal tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002659
-name: UVA radiation resistant
-synonym: "UV-A radiation resistant" EXACT [TyDI:56244]
-synonym: "UV-A resistant" EXACT [TyDI:56243]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002660
-name: UVA radiation sensitive
-synonym: "UV-A radiation sensitive" EXACT [TyDI:56276]
-synonym: "UV-A sensitive" EXACT [TyDI:56275]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002661
-name: UVA radiation tolerant
-synonym: "UV-A radiation tolerant" EXACT [TyDI:50781]
-synonym: "UV-A tolerant" EXACT [TyDI:50780]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002662
-name: UVB radiation resistant
-synonym: "UV-B radiation resistant" EXACT [TyDI:56304]
-synonym: "UV-B resistant" EXACT [TyDI:56303]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002663
-name: UVB radiation sensitive
-synonym: "UV-B radiation sensitive" EXACT [TyDI:56267]
-synonym: "UV-B sensitive" EXACT [TyDI:56268]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002664
-name: UVB radiation tolerant
-synonym: "UV-B radiation tolerant" EXACT [TyDI:50764]
-synonym: "UV-B tolerant" EXACT [TyDI:50765]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002665
-name: UVC radiation resistant
-synonym: "UV-C radiation resistant" EXACT [TyDI:56312]
-synonym: "UV-C resistant" EXACT [TyDI:56311]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002666
-name: UVC radiation sensitive
-synonym: "UV-C radiation sensitive" EXACT [TyDI:56288]
-synonym: "UV-C sensitive" EXACT [TyDI:56287]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002667
-name: UVC radiation tolerant
-synonym: "UV-C radiation tolerant" EXACT [TyDI:50759]
-synonym: "UV-C tolerant" EXACT [TyDI:50758]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002668
-name: animal commensal
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000239 ! commensal
-
-[Term]
-id: OBT:002669
-name: animal pathogen
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000375 ! pathogen
-
-[Term]
-id: OBT:002671
-name: antibacterial resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002672
-name: antibacterial sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002673
-name: antibacterial tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002674
-name: antibiotic resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000598 ! drug resistant
-
-[Term]
-id: OBT:002675
-name: antibiotic sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000599 ! drug sensitive
-
-[Term]
-id: OBT:002676
-name: antibiotic tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000600 ! drug tolerant
-
-[Term]
-id: OBT:002677
-name: antifungal resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002678
-name: antifungal sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002679
-name: antifungal tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002680
-name: antiviral resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002681
-name: antiviral sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002682
-name: antiviral tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002683
-name: antiyeast resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002684
-name: antiyeast sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002685
-name: antiyeast tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002711
-name: halotolerant
-is_a: OBT:000370 ! osmotolerant
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:002732
-name: phytopathogen
-synonym: "plant pathogen" EXACT [TyDI:58445]
-is_a: OBT:000375 ! pathogen
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:002733
-name: plant commensal
-is_a: OBT:000239 ! commensal
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:002734
-name: plant symbiont
-synonym: "phytosymbiont" EXACT [TyDI:58446]
-is_a: OBT:000394 ! plant hosted
-is_a: OBT:000441 ! symbiont
-
-[Term]
-id: OBT:002760
-name: aminoglycosides resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002761
-name: amoxicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002762
-name: ampicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002763
-name: ampicillin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002764
-name: animal opportunist
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000776 ! opportunistic pathogen
-
-[Term]
-id: OBT:002765
-name: antagonist
-is_a: OBT:002732 ! phytopathogen
-
-[Term]
-id: OBT:002772
-name: chloramphenicol resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002773
-name: ciprofloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002774
-name: ciprofloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002775
-name: ciprofloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002790
-name: erythromycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002792
-name: ethambutol resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002797
-name: gentamicin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002798
-name: gentamicin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002801
-name: glycopeptide antibiotics resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002806
-name: human pathogen
-is_a: OBT:002669 ! animal pathogen
-
-[Term]
-id: OBT:002809
-name: insect pathogen
-is_a: OBT:002669 ! animal pathogen
-
-[Term]
-id: OBT:002811
-name: isoniazid resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002817
-name: meticillin resistant
-synonym: "methicillin resistant" EXACT [TyDI:50715]
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002818
-name: meticillin sensitive
-synonym: "methicillin sensitive" EXACT [TyDI:56624]
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002819
-name: meticillin tolerant
-synonym: "methicillin tolerant" EXACT [TyDI:56655]
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002820
-name: moxifloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002821
-name: moxifloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002822
-name: moxifloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002823
-name: naladixic acid resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002824
-name: norfloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002825
-name: norfloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002826
-name: norfloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002827
-name: obligate phytopathogen
-is_a: OBT:002732 ! phytopathogen
-
-[Term]
-id: OBT:002829
-name: penicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002830
-name: penicillin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002831
-name: penicillin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002833
-name: plant facultative symbiont
-is_a: OBT:002734 ! plant symbiont
-
-[Term]
-id: OBT:002835
-name: plant obligate symbiont
-is_a: OBT:002734 ! plant symbiont
-
-[Term]
-id: OBT:002839
-name: pyrazinamide resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002840
-name: quinolone resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002843
-name: resistance to amikacin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002844
-name: resistance to cotrimoxazole
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002845
-name: resistance to dalfopristin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002846
-name: resistance to imipenem
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002847
-name: resistance to levofloxacin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002848
-name: resistance to quinupristin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002849
-name: rifampin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002857
-name: spectinomycin-resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002858
-name: streptomycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002861
-name: sulfamethoxazole resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002864
-name: susceptibility to azithromycin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002865
-name: susceptible to dalfopristin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002866
-name: susceptible to quinupristin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002867
-name: teicoplanin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002868
-name: teicoplanin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002869
-name: tetracycline resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002872
-name: trimethoprim resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002874
-name: vancomycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002875
-name: vancomycin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002876
-name: vancomycin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002881
-name: acido resistant
-synonym: "acid resistant" EXACT [TyDI:56703]
-synonym: "acidoresistant" EXACT [TyDI:56702]
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002882
-name: acido sensitive
-synonym: "acid sensitive" EXACT [TyDI:56747]
-synonym: "acidosensitive" EXACT [TyDI:56748]
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002883
-name: acido tolerant
-synonym: "acid tolerant" EXACT [TyDI:57294]
-synonym: "acidotolerant" EXACT [TyDI:57293]
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002886
-name: alkali resistant
-synonym: "alkaline resistant" EXACT [TyDI:56693]
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002887
-name: alkali sensitive
-synonym: "alkaline sensitive" RELATED [TyDI:56740]
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002888
-name: alkali tolerant
-synonym: "alkaline tolerant" RELATED [TyDI:53979]
-synonym: "alkalitolerant" EXACT [TyDI:53980]
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002895
-name: chemoheterotroph
-synonym: "chemo heterotroph " EXACT [TyDI:54366]
-is_a: OBT:000555 ! chemotroph
-is_a: OBT:000665 ! heterotroph
-
-[Term]
-id: OBT:002896
-name: chemolithotroph
-synonym: "chemo lithotroph " EXACT [TyDI:56147]
-is_a: OBT:000555 ! chemotroph
-is_a: OBT:000712 ! lithotroph
-
-[Term]
-id: OBT:002920
-name: oxacillin resistant
-is_a: OBT:002829 ! penicillin resistant
-
-[Term]
-id: OBT:002922
-name: photoautotroph
-synonym: "photo autotroph " EXACT [TyDI:54396]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002923
-name: photoheterotroph
-synonym: "photo heterotroph " EXACT [TyDI:54341]
-is_a: OBT:000665 ! heterotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002924
-name: photolithoautotroph
-synonym: "photo lithoautotroph" EXACT [TyDI:53974]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002945
-name: thermal resistant
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002955
-name: ammonia oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002959
-name: arsenic oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002975
-name: cold resistant
-synonym: "low temperature resistant" RELATED [TyDI:57099]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002982
-name: extreme cold resistant
-synonym: "extreme low temperature resistant" RELATED [TyDI:57106]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002983
-name: extreme heat resistant
-synonym: "extreme high temperature resistant" RELATED [TyDI:57032]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002984
-name: ferrous iron oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002985
-name: freeze-thaw resistant
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002987
-name: heat resistant
-synonym: "high temperature resistant" RELATED [TyDI:57091]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002991
-name: hydrogen oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003028
-name: sulfur oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003036
-name: anammox
-is_a: OBT:002955 ! ammonia oxidizing
-
-[Term]
-id: OBT:003038
-name: arsenite oxidizing
-is_a: OBT:002959 ! arsenic oxidizing
-
-[Term]
-id: OBT:003067
-name: petite positive
-synonym: "petite colony" EXACT [TyDI:50082]
-synonym: "petite mutant" EXACT [TyDI:50084]
-synonym: "petite strain" EXACT [TyDI:50083]
-synonym: "petite yeast" EXACT [TyDI:50081]
-is_a: OBT:000118 ! mutant
-is_a: OBT:000379 ! phenotype wrt carbon source
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:003125
-name: animal symbiont
-is_a: OBT:000441 ! symbiont
-is_a: OBT:002668 ! animal commensal
-
-[Term]
-id: OBT:003182
-name: animal facultative symbiont
-is_a: OBT:003125 ! animal symbiont
-
-[Term]
-id: OBT:003183
-name: animal obligate symbiont
-is_a: OBT:003125 ! animal symbiont
-
-[Term]
-id: OBT:003281
-name: chemo litho autotroph
-synonym: "lithoautotroph " EXACT [TyDI:54352]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003282
-name: chemoorganoheterotroph
-synonym: "chemo hetero organotroph" EXACT [TyDI:56150]
-synonym: "chemo organo heterotroph " EXACT [TyDI:56151]
-is_a: OBT:000778 ! organotroph
-is_a: OBT:002895 ! chemoheterotroph
-
-[Term]
-id: OBT:003299
-name: photoorganoheterotroph
-synonym: "photo organoheterotroph" EXACT [TyDI:56968]
-is_a: OBT:000778 ! organotroph
-is_a: OBT:002923 ! photoheterotroph
-
-[Term]
-id: OBT:003326
-name: saprophytic
-is_a: OBT:003282 ! chemoorganoheterotroph
-
-[Term]
-id: OBT:003445
-name: chemolithoheterotroph
-synonym: "chemo lithoheterotroph " EXACT [TyDI:54334]
-is_a: OBT:002895 ! chemoheterotroph
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003614
-name: cord-shaped
-is_a: OBT:000386 ! phenotype wrt shape
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-- 
GitLab


From 66a2b8a9d5f0703b736a95db2e880375bae22b84 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Thu, 4 Mar 2021 12:49:32 +0000
Subject: [PATCH 63/64] Delete BioNLP-OST+EnovFood-no-obsolete.obo

---
 .../BioNLP-OST+EnovFood-no-obsolete.obo       | 22829 ----------------
 1 file changed, 22829 deletions(-)
 delete mode 100644 ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo

diff --git a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo b/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
deleted file mode 100644
index 9a9716d4..00000000
--- a/ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo
+++ /dev/null
@@ -1,22829 +0,0 @@
-format-version: 1.2
-date: 25:02:2021 17:05
-saved-by: claire
-auto-generated-by: OBO-Edit 2.3.1
-
-[Term]
-id: OBT:000000
-name: root for extraction
-
-[Term]
-id: OBT:000001
-name: microbial habitat
-is_a: OBT:000000 ! root for extraction
-
-[Term]
-id: OBT:000002
-name: microbial phenotype
-is_a: OBT:000000 ! root for extraction
-
-[Term]
-id: OBT:000003
-name: animal habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000004
-name: animal husbandry and agricultural habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000005
-name: aquaculture habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000006
-name: artificial environment
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000007
-name: experimental medium
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000008
-name: food
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000009
-name: habitat wrt chemico-physical property
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000010
-name: living organism
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000011
-name: medical environment
-synonym: "clinical" RELATED [TyDI:52464]
-synonym: "nosocomial" RELATED [TyDI:52463]
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000012
-name: microorganism associated habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000013
-name: natural environment habitat
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000014
-name: part of living organism
-synonym: "host part" RELATED [TyDI:52452]
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000015
-name: phenotype wrt adhesion
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000016
-name: phenotype wrt community behaviour
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000017
-name: phenotype wrt environment
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000018
-name: phenotype wrt growth
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000019
-name: phenotype wrt metabolic activity
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000020
-name: phenotype wrt morphology
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000021
-name: phenotype wrt motility
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000022
-name: phenotype wrt ploidy
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000023
-name: phenotype wrt stress
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000024
-name: phenotype wrt genetic
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000025
-name: physiological phenotype
-is_a: OBT:000002 ! microbial phenotype
-
-[Term]
-id: OBT:000026
-name: planet
-is_a: OBT:000001 ! microbial habitat
-
-[Term]
-id: OBT:000027
-name: Earth
-is_a: OBT:000026 ! planet
-
-[Term]
-id: OBT:000028
-name: L-( null )-tartrate enriched soil
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000029
-name: adherent
-is_a: OBT:000015 ! phenotype wrt adhesion
-
-[Term]
-id: OBT:000030
-name: aerosol
-synonym: "aerosolized" RELATED [TyDI:53259]
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000031
-name: agar
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000032
-name: agricultural equipment
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000033
-name: agricultural input
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000034
-name: agricultural product
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000035
-name: agricultural species
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000036
-name: alloploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000037
-name: aneuploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000038
-name: animal feed
-synonym: "animal food" RELATED [TyDI:52402]
-synonym: "zoo animal's food" RELATED [TyDI:52401]
-is_a: OBT:000008 ! food
-
-[Term]
-id: OBT:000039
-name: animal part
-synonym: "animal host part" RELATED [TyDI:53074]
-synonym: "body part" RELATED [TyDI:53075]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000040
-name: anoxygenic
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000041
-name: antibiotic-containing media
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000042
-name: antimicrobial activity
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000043
-name: apiary
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000044
-name: aquaculture equipment
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000045
-name: aquaculture farm
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000046
-name: aquaculture pond
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000047
-name: aquatic environment
-synonym: "aquatic" RELATED [TyDI:53034]
-synonym: "aquatic habitat" RELATED [TyDI:53033]
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000048
-name: area with climate property
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000049
-name: area with epidemiologic property
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000050
-name: artificial water environment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000051
-name: asexual reproduction
-synonym: "asexual growth" EXACT [TyDI:50000]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000052
-name: atmosphere part
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000053
-name: autoploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000054
-name: biofilm
-synonym: "microbial slime" RELATED [TyDI:53290]
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000055
-name: bioluminescent
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000056
-name: bioreactor
-synonym: "biofilm reactor" EXACT []
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000057
-name: bloom forming
-synonym: "bloom-forming" EXACT [TyDI:56194]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000058
-name: bovine serum
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000059
-name: breeding site
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000060
-name: catalase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000061
-name: cell
-synonym: "cellular" EXACT [TyDI:53156]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000062
-name: cell culture
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000063
-name: coagulase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000064
-name: colony morphology phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000065
-name: conjugation phenotype
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000066
-name: constructed habitat
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000067
-name: cultivated habitat
-synonym: "cultivated area" EXACT []
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000068
-name: decarboxylase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000069
-name: diploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000070
-name: endolithic
-synonym: "endolith" EXACT [TyDI:58450]
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000071
-name: endolython
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000072
-name: endopelic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000073
-name: endopelon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000074
-name: endophyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000075
-name: endopsammic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000076
-name: endopsammon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000077
-name: endozoon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000078
-name: environment wrt oxygen level
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000079
-name: environmental matter
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000080
-name: epilythic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000081
-name: epilython
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000082
-name: epipelic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000083
-name: epipelon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000084
-name: epipsammic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000085
-name: epipsammon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000086
-name: epixylic
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000087
-name: epixylon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000088
-name: epizoon
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000089
-name: eukaryote host
-synonym: "eukaryote" RELATED [TyDI:53285]
-synonym: "eukaryotic" RELATED [TyDI:53283]
-synonym: "eukaryotic host" EXACT [TyDI:53284]
-synonym: "host" RELATED [TyDI:53282]
-is_a: OBT:000010 ! living organism
-
-[Term]
-id: OBT:000090
-name: extreme environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000091
-name: farm
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000092
-name: field
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000093
-name: fish pond
-synonym: "fish culture pond" EXACT [TyDI:53118]
-is_a: OBT:000005 ! aquaculture habitat
-
-[Term]
-id: OBT:000094
-name: food for human
-synonym: "agro-alimentary environment" EXACT [TyDI:53274]
-synonym: "alimentary" RELATED [TyDI:53273]
-synonym: "food product" EXACT [TyDI:53272]
-synonym: "foodborne" RELATED [TyDI:53275]
-is_a: OBT:000008 ! food
-
-[Term]
-id: OBT:000095
-name: greenhouse
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000096
-name: haploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000097
-name: hospital environment
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000098
-name: household good
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000099
-name: hyphae growth
-synonym: "hyphae" EXACT [TyDI:49986]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000100
-name: industrial habitat
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000101
-name: intercellular
-synonym: "intercellularly" RELATED [TyDI:53082]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000102
-name: iron-rich environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000103
-name: laboratory equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000104
-name: lichen forming
-synonym: "lichen-forming" EXACT [TyDI:56235]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000105
-name: liquid culture morphology phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000106
-name: liquid medium
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000107
-name: lytic
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000108
-name: medical equipment
-synonym: "medical care equipment" RELATED [TyDI:53027]
-synonym: "medical care supply" RELATED [TyDI:53029]
-synonym: "medical device" RELATED [TyDI:53030]
-synonym: "medical supply" RELATED [TyDI:53028]
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000109
-name: medical product
-is_a: OBT:000011 ! medical environment
-
-[Term]
-id: OBT:000110
-name: medical sample
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000111
-name: metaphyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000112
-name: microbial mat layer
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000113
-name: microflora
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000114
-name: microorganism
-synonym: "microbe" EXACT [TyDI:52385]
-synonym: "microbial" RELATED [TyDI:52386]
-is_a: OBT:000010 ! living organism
-
-[Term]
-id: OBT:000115
-name: microorganism part
-synonym: "microbe part" RELATED [TyDI:52345]
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000116
-name: microscopic morphological phenotype
-is_a: OBT:000020 ! phenotype wrt morphology
-
-[Term]
-id: OBT:000117
-name: motile
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000118
-name: mutant
-is_a: OBT:000024 ! phenotype wrt genetic
-
-[Term]
-id: OBT:000119
-name: nest
-is_a: OBT:000003 ! animal habitat
-
-[Term]
-id: OBT:000120
-name: non motile
-synonym: "non-motile" EXACT [TyDI:54838]
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000121
-name: non-immune serum
-synonym: "nonimmune serum" EXACT [TyDI:52417]
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000122
-name: non-sporulating
-synonym: "non spore forming" RELATED [TyDI:51017]
-synonym: "non sporulating" RELATED [TyDI:51016]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000123
-name: oxidoreductase activity
-is_a: OBT:000019 ! phenotype wrt metabolic activity
-
-[Term]
-id: OBT:000124
-name: periphyton
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000125
-name: phenotype wrt disease impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000126
-name: phenotype wrt energy source
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000127
-name: phenotype wrt habitat acidity
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000128
-name: phenotype wrt habitat osmolarity
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000129
-name: phenotype wrt habitat oxygen
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000130
-name: phenotype wrt habitat temperature
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000131
-name: phenotype wrt immune system impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000132
-name: phenotype wrt microbial-host interaction
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000133
-name: phenotype wrt molecule impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000134
-name: phenotype wrt nutrient abundance
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000135
-name: phenotype wrt pressure
-is_a: OBT:000025 ! physiological phenotype
-
-[Term]
-id: OBT:000136
-name: phenotype wrt radiation impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000137
-name: phenotype wrt relative humidity impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000138
-name: phenotype wrt temperature impact
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000139
-name: planktonic
-synonym: "free floating" EXACT [TyDI:57519]
-is_a: OBT:000015 ! phenotype wrt adhesion
-
-[Term]
-id: OBT:000140
-name: plant habitat
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000141
-name: polluted environment
-synonym: "contaminated site" RELATED [TyDI:52368]
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000142
-name: presence of nanotube
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000143
-name: presence of quorum sensing
-synonym: "quorum sensing" RELATED [TyDI:57709]
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000144
-name: pseudohyphae growth
-synonym: "pseudohyphae" EXACT [TyDI:49979]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000145
-name: public equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000146
-name: rural area
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000147
-name: sexual mating
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:000148
-name: sexual reproduction
-synonym: "asci formation" EXACT [TyDI:49995]
-synonym: "ascospore formation" EXACT [TyDI:49997]
-synonym: "ascus formation" EXACT [TyDI:49996]
-synonym: "meiospore formation" RELATED [TyDI:49994]
-synonym: "sexual growth" EXACT [TyDI:49993]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000149
-name: spore
-is_a: OBT:000014 ! part of living organism
-
-[Term]
-id: OBT:000150
-name: sporulating
-synonym: "endospore forming" RELATED [TyDI:57325]
-synonym: "endospore-forming" RELATED [TyDI:57324]
-synonym: "spore forming" EXACT [TyDI:57323]
-synonym: "spore liberation" EXACT [TyDI:57322]
-synonym: "spore-forming" EXACT [TyDI:57321]
-is_a: OBT:000018 ! phenotype wrt growth
-
-[Term]
-id: OBT:000151
-name: sterile water
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000152
-name: stress resistant
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000153
-name: stress sensitive
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000154
-name: stress tolerant
-is_a: OBT:000023 ! phenotype wrt stress
-
-[Term]
-id: OBT:000155
-name: stromatolite
-is_a: OBT:000012 ! microorganism associated habitat
-
-[Term]
-id: OBT:000156
-name: subterrestrial habitat
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000157
-name: taxis phenotype
-is_a: OBT:000021 ! phenotype wrt motility
-
-[Term]
-id: OBT:000158
-name: terrestrial habitat
-synonym: "terrestrial" RELATED [TyDI:53216]
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000159
-name: tetraploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000160
-name: thermal area
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000161
-name: transport and storage equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000162
-name: transport equipment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000163
-name: triploid
-is_a: OBT:000022 ! phenotype wrt ploidy
-
-[Term]
-id: OBT:000164
-name: ubiquitous
-is_a: OBT:000017 ! phenotype wrt environment
-
-[Term]
-id: OBT:000165
-name: urea solution
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000166
-name: volcanic area
-is_a: OBT:000013 ! natural environment habitat
-
-[Term]
-id: OBT:000167
-name: waste treatment environment
-is_a: OBT:000006 ! artificial environment
-
-[Term]
-id: OBT:000168
-name: wet environment
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-
-[Term]
-id: OBT:000169
-name: wild-type
-synonym: "wild type" EXACT [TyDI:49976]
-is_a: OBT:000024 ! phenotype wrt genetic
-
-[Term]
-id: OBT:000170
-name: yeast extract
-is_a: OBT:000007 ! experimental medium
-
-[Term]
-id: OBT:000171
-name: zoo
-synonym: "zoo garden" RELATED [TyDI:55262]
-synonym: "zoo park" RELATED [TyDI:55261]
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:000172
-name: MATa
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000173
-name: MATalpha
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000174
-name: Neisser stain phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000175
-name: abdomen
-synonym: "abdominal" RELATED [TyDI:55839]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000176
-name: acid environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000177
-name: acidophile
-synonym: "acidophilic " EXACT [TyDI:56123]
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000178
-name: adipocyte
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000179
-name: aerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000180
-name: aerobic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000181
-name: aerobic environment
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000182
-name: aerotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000183
-name: aerotolerant
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000184
-name: agricultural pest
-is_a: OBT:000035 ! agricultural species
-
-[Term]
-id: OBT:000185
-name: agricultural tool
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000186
-name: air
-synonym: "atmospheric" EXACT [TyDI:53125]
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000187
-name: alkaline environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000188
-name: alkaliphile
-synonym: "alkaliphilic " EXACT [TyDI:56126]
-synonym: "alkalophile " EXACT [TyDI:56127]
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000189
-name: anaerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000190
-name: anaerobic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000191
-name: anaerobic environment
-synonym: "anoxic environments" EXACT [TyDI:55774]
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000192
-name: anemotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000193
-name: animal
-synonym: "animal host" RELATED [TyDI:54803]
-synonym: "animal species" RELATED [TyDI:54805]
-synonym: "animal-associated habitat" EXACT [TyDI:54804]
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000194
-name: animal farm
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000195
-name: animal hosted
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000196
-name: animal tissue
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000197
-name: anoxic environment
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000198
-name: aquarium
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000199
-name: aquatic eukaryotic species
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000200
-name: arthropod part
-synonym: "arthropod organ" EXACT [TyDI:52938]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000201
-name: artificial water structure
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000202
-name: automated teller machine
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:000203
-name: auxotroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000204
-name: back
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000205
-name: bandage
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000206
-name: banknote
-synonym: "bank note" EXACT [TyDI:56443]
-synonym: "currency note" EXACT [TyDI:56444]
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000207
-name: barotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000208
-name: bathroom equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000209
-name: beak
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000210
-name: bedroom equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000211
-name: bile resistant
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:000212
-name: biofilm in natural environment
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000213
-name: biomat
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000214
-name: body
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000215
-name: body fluid
-synonym: "bodily fluid" EXACT [TyDI:55885]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000216
-name: body surface
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000217
-name: boot swab
-synonym: "overshoe" RELATED [TyDI:57230]
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000218
-name: carboxydotroph
-synonym: "carboxydotrophic " EXACT [TyDI:54401]
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000219
-name: carpet
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000220
-name: carpet tile
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000221
-name: catalase negative
-synonym: "catalase -" RELATED [TyDI:57877]
-is_a: OBT:000060 ! catalase activity
-
-[Term]
-id: OBT:000222
-name: catalase positive
-synonym: "catalase +" RELATED [TyDI:57872]
-is_a: OBT:000060 ! catalase activity
-
-[Term]
-id: OBT:000223
-name: catheter
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000224
-name: cattle-dipping vat
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000225
-name: cave
-is_a: OBT:000156 ! subterrestrial habitat
-
-[Term]
-id: OBT:000226
-name: ceiling tile
-is_a: OBT:003617 ! environmental surface
-
-[Term]
-id: OBT:000227
-name: cell sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000228
-name: cellular shape phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000229
-name: cereal feed
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000230
-name: chemotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000231
-name: circulatory system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000232
-name: city
-synonym: "urban area" EXACT [TyDI:55802]
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000233
-name: cloud
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000234
-name: cloud water
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000235
-name: coagulase negative
-is_a: OBT:000063 ! coagulase activity
-
-[Term]
-id: OBT:000236
-name: coagulase positive
-is_a: OBT:000063 ! coagulase activity
-
-[Term]
-id: OBT:000237
-name: coelomic cavity
-synonym: "coelom" EXACT [TyDI:55848]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000238
-name: cold temperature environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000239
-name: commensal
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000240
-name: commodity and primary derivative thereof
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000241
-name: composting reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000242
-name: conidial
-is_a: OBT:000150 ! sporulating
-
-[Term]
-id: OBT:000243
-name: conjugating
-is_a: OBT:000065 ! conjugation phenotype
-
-[Term]
-id: OBT:000244
-name: contaminated site
-is_a: OBT:000141 ! polluted environment
-
-[Term]
-id: OBT:000245
-name: copiotrophic
-synonym: "copiotroph " EXACT [TyDI:54275]
-is_a: OBT:000134 ! phenotype wrt nutrient abundance
-
-[Term]
-id: OBT:000246
-name: crop
-is_a: OBT:000034 ! agricultural product
-
-[Term]
-id: OBT:000247
-name: cruise ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000248
-name: cryophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000249
-name: cyanide treatment bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000250
-name: dairy farm equipment
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000251
-name: decarboxylase negative
-is_a: OBT:000068 ! decarboxylase activity
-
-[Term]
-id: OBT:000252
-name: decarboxylase positive
-is_a: OBT:000068 ! decarboxylase activity
-
-[Term]
-id: OBT:000253
-name: deep subsurface
-is_a: OBT:000156 ! subterrestrial habitat
-
-[Term]
-id: OBT:000254
-name: denitrification reactor
-synonym: "denitrifying reactor" EXACT [TyDI:55216]
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000255
-name: dental chair
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000256
-name: diagnostic equipment
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000257
-name: diazotroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000258
-name: digestive system part
-synonym: "digestive tract part" EXACT [TyDI:54661]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000259
-name: ditch water
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000260
-name: domestic appliance
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000261
-name: drug
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000262
-name: durotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000263
-name: dust
-synonym: "dust particle" EXACT [TyDI:54762]
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000264
-name: ear part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000265
-name: electrotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000266
-name: endolithic environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000267
-name: endosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000268
-name: enterocyte
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000269
-name: environment water
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000270
-name: exoskeleton
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000271
-name: exosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000272
-name: extra-genital
-synonym: "extragenital" EXACT [TyDI:54812]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000273
-name: extra-intestinal
-synonym: "extraintestinal" EXACT [TyDI:54796]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000274
-name: extracellular
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000275
-name: extreme thermophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000276
-name: extremely acidophilic
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000277
-name: eye part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000278
-name: facultative aerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000279
-name: facultative anaerobe
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000280
-name: feeder cell
-is_a: OBT:000062 ! cell culture
-
-[Term]
-id: OBT:000281
-name: fertilizer
-is_a: OBT:000033 ! agricultural input
-
-[Term]
-id: OBT:000282
-name: finger
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000283
-name: fish pen
-synonym: "fish cage" EXACT [TyDI:55874]
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000284
-name: flagellum
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000285
-name: flesh
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000286
-name: flocculent
-synonym: "flocculant" EXACT [TyDI:57333]
-synonym: "flocculating" EXACT [TyDI:57332]
-is_a: OBT:000105 ! liquid culture morphology phenotype
-
-[Term]
-id: OBT:000287
-name: forage
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000288
-name: free-living
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000289
-name: freight transport equipment
-synonym: "good transport equipment" RELATED [TyDI:58103]
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000290
-name: fungi
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000291
-name: furniture
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000292
-name: garden
-is_a: OBT:000067 ! cultivated habitat
-
-[Term]
-id: OBT:000293
-name: geothermal area
-is_a: OBT:000160 ! thermal area
-
-[Term]
-id: OBT:000294
-name: germ cell
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000295
-name: gliding
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000296
-name: gram stain phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000297
-name: granular
-is_a: OBT:000105 ! liquid culture morphology phenotype
-
-[Term]
-id: OBT:000298
-name: granuloma
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000299
-name: grassland
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:000300
-name: gravitactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000301
-name: hair
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000302
-name: haline environment
-synonym: "salty environment" RELATED [TyDI:55698]
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000303
-name: hatchery
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000304
-name: hemolytic
-synonym: "haemolytic" EXACT [TyDI:58363]
-is_a: OBT:000107 ! lytic
-
-[Term]
-id: OBT:000305
-name: heterothallic
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000306
-name: high osmolarity environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000307
-name: high pressure environment
-synonym: "high-pressure biotope" EXACT [TyDI:55693]
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000308
-name: high sulfur concentration environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000309
-name: high temperature environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000310
-name: homothallic
-is_a: OBT:000147 ! sexual mating
-
-[Term]
-id: OBT:000311
-name: horticulture farm
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000312
-name: hospital water
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000313
-name: host associated biofilm
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000314
-name: hotel equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000315
-name: house
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000316
-name: household product
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000317
-name: hydrotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000318
-name: hydrotelluric environment
-synonym: "hydro-telluric" RELATED [TyDI:54758]
-synonym: "hydrotelluric" RELATED [TyDI:54759]
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000319
-name: hyperthermophile
-synonym: "extreme thermophile" RELATED [TyDI:56138]
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000320
-name: immune cell
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000321
-name: immune system
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000322
-name: industrial chemical
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000323
-name: industrial product
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000324
-name: industrial site
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000325
-name: industrial water and effluent
-is_a: OBT:000100 ! industrial habitat
-
-[Term]
-id: OBT:000326
-name: inland water body
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000327
-name: inside the body
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000328
-name: intensive care unit
-synonym: "ICU" EXACT [TyDI:54787]
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000329
-name: intracellular
-synonym: "intracellularly" RELATED [TyDI:50847]
-is_a: OBT:000061 ! cell
-
-[Term]
-id: OBT:000330
-name: kitchen equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000331
-name: landfill
-is_a: OBT:000167 ! waste treatment environment
-
-[Term]
-id: OBT:000332
-name: lesion
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000333
-name: lower layer of a microbial mat
-is_a: OBT:000112 ! microbial mat layer
-
-[Term]
-id: OBT:000334
-name: lymphatic system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000335
-name: magnetotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000336
-name: mariculture farm
-is_a: OBT:000045 ! aquaculture farm
-
-[Term]
-id: OBT:000337
-name: marine cage
-is_a: OBT:000044 ! aquaculture equipment
-
-[Term]
-id: OBT:000338
-name: marine environment
-synonym: "marine" RELATED [TyDI:52984]
-synonym: "marine area" RELATED [TyDI:52987]
-synonym: "ocean" RELATED [TyDI:52986]
-synonym: "oceanic" RELATED [TyDI:52988]
-synonym: "sea" RELATED [TyDI:52985]
-is_a: OBT:000047 ! aquatic environment
-
-[Term]
-id: OBT:000339
-name: meal
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000340
-name: meat and bone meal
-is_a: OBT:000038 ! animal feed
-
-[Term]
-id: OBT:000341
-name: medical outfit
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000342
-name: medical sink
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000343
-name: mesophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000344
-name: mesosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000345
-name: metallic coin
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000346
-name: methanogenic reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000347
-name: microaerophile
-is_a: OBT:000129 ! phenotype wrt habitat oxygen
-
-[Term]
-id: OBT:000348
-name: microaerophilic environment
-synonym: "hypoxic environment" RELATED [TyDI:55783]
-is_a: OBT:000078 ! environment wrt oxygen level
-
-[Term]
-id: OBT:000349
-name: microorganism gas vesicle
-is_a: OBT:000115 ! microorganism part
-
-[Term]
-id: OBT:000350
-name: mineral matter
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000351
-name: mire
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000352
-name: monument
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000353
-name: multicellular arrangement phenotype
-is_a: OBT:000116 ! microscopic morphological phenotype
-
-[Term]
-id: OBT:000354
-name: mushroom farm
-synonym: "mushroom factory" RELATED [TyDI:55316]
-synonym: "mushroom factory farm" EXACT [TyDI:55315]
-is_a: OBT:000091 ! farm
-
-[Term]
-id: OBT:000355
-name: naval surface ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000356
-name: needle
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000357
-name: nervous system part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000358
-name: neuston
-synonym: "neuston biofilm" EXACT [TyDI:54784]
-is_a: OBT:000054 ! biofilm
-
-[Term]
-id: OBT:000359
-name: neutralophile
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:000360
-name: nutrient broth
-is_a: OBT:000106 ! liquid medium
-
-[Term]
-id: OBT:000361
-name: oligotrophic
-synonym: "oligotroph " EXACT [TyDI:54278]
-is_a: OBT:000134 ! phenotype wrt nutrient abundance
-
-[Term]
-id: OBT:000362
-name: oomycete
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000363
-name: operating room
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000364
-name: organ
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000365
-name: organic matter
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000366
-name: oropharynx
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000367
-name: osmophile
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000368
-name: osmophobe
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000369
-name: osmotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000370
-name: osmotolerant
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000371
-name: oxidase activity
-is_a: OBT:000123 ! oxidoreductase activity
-
-[Term]
-id: OBT:000372
-name: parasite
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000373
-name: part of food
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000374
-name: pasture
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:000375
-name: pathogen
-synonym: "infectious agent" EXACT [TyDI:54923]
-synonym: "virulence phenotype" EXACT [TyDI:54924]
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000376
-name: perineum
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000377
-name: peritoneal cavity
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000378
-name: phenotype wrt antimicrobial impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000379
-name: phenotype wrt carbon source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000380
-name: phenotype wrt color
-is_a: OBT:000064 ! colony morphology phenotype
-
-[Term]
-id: OBT:000381
-name: phenotype wrt drug impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000382
-name: phenotype wrt habitat salinity
-is_a: OBT:000128 ! phenotype wrt habitat osmolarity
-
-[Term]
-id: OBT:000383
-name: phenotype wrt living energy source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000384
-name: phenotype wrt metal concentration impact
-is_a: OBT:000133 ! phenotype wrt molecule impact
-
-[Term]
-id: OBT:000385
-name: phenotype wrt reducing equivalent source
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000386
-name: phenotype wrt shape
-is_a: OBT:000064 ! colony morphology phenotype
-
-[Term]
-id: OBT:000387
-name: phototactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000388
-name: phyllosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000389
-name: phyllosphere part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000390
-name: piezophile
-synonym: "barophile " EXACT [TyDI:54198]
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000391
-name: piezosensitive
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000392
-name: piezotolerant
-synonym: "barotolerant " EXACT [TyDI:54205]
-is_a: OBT:000135 ! phenotype wrt pressure
-
-[Term]
-id: OBT:000393
-name: plant
-synonym: "green plant" EXACT [TyDI:54809]
-synonym: "host plant" RELATED [TyDI:54808]
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000394
-name: plant hosted
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000395
-name: plant part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000396
-name: pore forming
-is_a: OBT:000107 ! lytic
-
-[Term]
-id: OBT:000397
-name: prepared food
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000398
-name: prosthesis
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000399
-name: prototroph
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000400
-name: protozoa
-is_a: OBT:000089 ! eukaryote host
-
-[Term]
-id: OBT:000401
-name: psychrophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000402
-name: psychrotrophic
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000403
-name: public building
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000404
-name: public toilet
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:000405
-name: public transport
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000406
-name: recreational fishing fish pond
-is_a: OBT:000093 ! fish pond
-
-[Term]
-id: OBT:000407
-name: respiratory tract
-synonym: "respiratory" RELATED [TyDI:55563]
-synonym: "respiratory airway" RELATED []
-synonym: "respiratory tree" RELATED [TyDI:55564]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000408
-name: respiratory tract part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000409
-name: rheotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000410
-name: rhizosphere
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000411
-name: rhizosphere part
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000412
-name: road part
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000413
-name: rodent nest
-is_a: OBT:000119 ! nest
-
-[Term]
-id: OBT:000414
-name: room
-is_a: OBT:000066 ! constructed habitat
-
-[Term]
-id: OBT:000415
-name: room floor
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000416
-name: salivary sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000417
-name: sessile
-is_a: OBT:000029 ! adherent
-
-[Term]
-id: OBT:000418
-name: ship
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000419
-name: ship hull
-is_a: OBT:000162 ! transport equipment
-
-[Term]
-id: OBT:000420
-name: shoe
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000421
-name: shower aerosol
-is_a: OBT:000030 ! aerosol
-
-[Term]
-id: OBT:000422
-name: shrimp culture pond
-synonym: "shrimp pond" EXACT [TyDI:54781]
-is_a: OBT:000046 ! aquaculture pond
-
-[Term]
-id: OBT:000423
-name: silo
-is_a: OBT:000032 ! agricultural equipment
-
-[Term]
-id: OBT:000424
-name: skin part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000425
-name: slough
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000426
-name: sludge blanket reactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000427
-name: soil
-synonym: "soilborne" EXACT [TyDI:55680]
-is_a: OBT:000158 ! terrestrial habitat
-
-[Term]
-id: OBT:000428
-name: soil part
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000429
-name: solfatara
-synonym: "fumarole field" RELATED [TyDI:55674]
-synonym: "solfatara field" RELATED [TyDI:55673]
-is_a: OBT:000166 ! volcanic area
-
-[Term]
-id: OBT:000430
-name: spoiled food
-synonym: "contaminated food" RELATED [TyDI:50976]
-is_a: OBT:000094 ! food for human
-
-[Term]
-id: OBT:000431
-name: sputum sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000432
-name: starter culture
-synonym: "dry starter" RELATED [TyDI:52942]
-synonym: "starter" EXACT []
-is_a: OBT:000113 ! microflora
-
-[Term]
-id: OBT:000433
-name: sterile clean room
-is_a: OBT:000097 ! hospital environment
-
-[Term]
-id: OBT:000434
-name: storage equipment
-is_a: OBT:000161 ! transport and storage equipment
-created_by: claire
-creation_date: 2019-05-27T16:40:36Z
-
-[Term]
-id: OBT:000435
-name: stratosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000436
-name: subtropical area
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000437
-name: sulfide-rich environment
-is_a: OBT:000090 ! extreme environment
-
-[Term]
-id: OBT:000438
-name: surgical drain
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000439
-name: swarming
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000440
-name: swimming
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000441
-name: symbiont
-is_a: OBT:000132 ! phenotype wrt microbial-host interaction
-
-[Term]
-id: OBT:000442
-name: symbiosome
-is_a: OBT:000140 ! plant habitat
-
-[Term]
-id: OBT:000443
-name: syntrophic
-is_a: OBT:000126 ! phenotype wrt energy source
-
-[Term]
-id: OBT:000444
-name: syringe
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000445
-name: temperate zone
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000446
-name: terrestrial landscape
-is_a: OBT:000158 ! terrestrial habitat
-
-[Term]
-id: OBT:000447
-name: textile
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000448
-name: therapeutic equipment
-synonym: "therapy equipment" EXACT [TyDI:55458]
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:000449
-name: thermophile
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000450
-name: thermophilic methanogenic bioreactor
-is_a: OBT:000056 ! bioreactor
-
-[Term]
-id: OBT:000451
-name: thermosphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000452
-name: thermotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000453
-name: thermotolerant
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-
-[Term]
-id: OBT:000454
-name: thigmotactic
-is_a: OBT:000157 ! taxis phenotype
-
-[Term]
-id: OBT:000455
-name: toilet equipment
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000456
-name: transconjugating
-synonym: "transconjugant" RELATED [TyDI:50685]
-is_a: OBT:000065 ! conjugation phenotype
-
-[Term]
-id: OBT:000457
-name: traveller luggage
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000458
-name: tropical zone
-synonym: "tropical area" EXACT [TyDI:55365]
-is_a: OBT:000048 ! area with climate property
-
-[Term]
-id: OBT:000459
-name: troposphere
-is_a: OBT:000052 ! atmosphere part
-
-[Term]
-id: OBT:000460
-name: twitching
-is_a: OBT:000117 ! motile
-
-[Term]
-id: OBT:000461
-name: ultrasound gel
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000462
-name: urine sediment
-is_a: OBT:000110 ! medical sample
-
-[Term]
-id: OBT:000463
-name: urogenital tract part
-synonym: "genitourinary system part" RELATED [TyDI:55857]
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000464
-name: vaccine
-is_a: OBT:000109 ! medical product
-
-[Term]
-id: OBT:000465
-name: vertebrate part
-is_a: OBT:000039 ! animal part
-
-[Term]
-id: OBT:000466
-name: wall
-synonym: "mural" RELATED [TyDI:56537]
-is_a: OBT:000098 ! household good
-
-[Term]
-id: OBT:000467
-name: waste
-is_a: OBT:000167 ! waste treatment environment
-
-[Term]
-id: OBT:000468
-name: water
-is_a: OBT:000079 ! environmental matter
-
-[Term]
-id: OBT:000469
-name: water well
-is_a: OBT:000050 ! artificial water environment
-
-[Term]
-id: OBT:000470
-name: Glomus vesiculiferum
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000471
-name: Intestinal mucosal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000472
-name: Neisser-negative
-synonym: "Neisser -" RELATED [TyDI:57819]
-is_a: OBT:000174 ! Neisser stain phenotype
-
-[Term]
-id: OBT:000473
-name: Neisser-positive
-synonym: "Neisser +" RELATED [TyDI:57816]
-is_a: OBT:000174 ! Neisser stain phenotype
-
-[Term]
-id: OBT:000474
-name: Saccharomyces cerevisiae starter
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000475
-name: abrasion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000476
-name: abscess
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000477
-name: additive
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000478
-name: agricultural waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000479
-name: air treatment unit
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000480
-name: airplane
-synonym: "aeroplane" RELATED [TyDI:55951]
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000481
-name: airport terminal
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000482
-name: alpha-hemolytic
-is_a: OBT:000304 ! hemolytic
-
-[Term]
-id: OBT:000483
-name: alpine soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000484
-name: alveolar epithelium
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000485
-name: amniotic fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000486
-name: amoebas
-is_a: OBT:000400 ! protozoa
-
-[Term]
-id: OBT:000487
-name: anaerobic dechlorinating bioreactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000488
-name: anaerobic sludge blanket reactor
-synonym: "UASB reactor" EXACT []
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000489
-name: animal product and primary derivative thereof
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000490
-name: animal with age or sex property
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000491
-name: animal with disease
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000492
-name: antacid suspension
-is_a: OBT:000261 ! drug
-
-[Term]
-id: OBT:000493
-name: anthosphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000494
-name: anthosphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000495
-name: aqueous humour
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000496
-name: arthropod
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000497
-name: atherosclerotic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000498
-name: auricular prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000499
-name: autotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000500
-name: bacteriocyte
-is_a: OBT:000178 ! adipocyte
-
-[Term]
-id: OBT:000501
-name: barley feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000502
-name: bathroom
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000503
-name: bathroom sink
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000504
-name: bathtub
-synonym: "bath tub" EXACT []
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000505
-name: bay
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000506
-name: bed as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000507
-name: bed sheet
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000508
-name: bedroom
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000509
-name: bedspread
-synonym: "bed cover" RELATED [TyDI:52109]
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000510
-name: beef farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000511
-name: beer yeast
-synonym: "brewer yeast" EXACT [TyDI:51000]
-synonym: "brewer's yeast" EXACT [TyDI:50998]
-synonym: "brewery yeast" EXACT [TyDI:51001]
-synonym: "brewing yeast" EXACT [TyDI:50999]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000512
-name: beta-hemolytic
-is_a: OBT:000304 ! hemolytic
-
-[Term]
-id: OBT:000513
-name: big colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000514
-name: bile
-synonym: "gall" RELATED [TyDI:57924]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000515
-name: biliary tract
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000516
-name: biofertilizer
-is_a: OBT:000281 ! fertilizer
-
-[Term]
-id: OBT:000517
-name: biotrophic
-synonym: "obligate biotrophic " EXACT [TyDI:55611]
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000518
-name: bladder
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000519
-name: bladder stone
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000520
-name: blender
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000521
-name: blood
-synonym: "blood stream" RELATED [TyDI:58013]
-synonym: "bloodstream" RELATED [TyDI:58012]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000522
-name: blood meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000523
-name: blood plasma
-synonym: "plasma" RELATED [TyDI:57935]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000524
-name: blood serum
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000525
-name: blood vessel
-synonym: "vein" EXACT [TyDI:52363]
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000526
-name: bone fracture
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000527
-name: bone meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000528
-name: bone-anchored prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000529
-name: broncho-pulmonary segment
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000530
-name: bronchus
-synonym: "branchial" RELATED [TyDI:50479]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000531
-name: buffet
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000532
-name: building construction and demolition waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000533
-name: bulk soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000534
-name: bulk tank
-synonym: "bulk milk cooling tank" EXACT [TyDI:57148]
-synonym: "milk cooler" EXACT [TyDI:57149]
-is_a: OBT:000250 ! dairy farm equipment
-
-[Term]
-id: OBT:000535
-name: burn
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000536
-name: canker
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000537
-name: carcass
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000538
-name: caries
-synonym: "caries lesion" RELATED [TyDI:57836]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000539
-name: carpet floor
-is_a: OBT:000415 ! room floor
-
-[Term]
-id: OBT:000540
-name: carposphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000541
-name: carposphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000542
-name: carrier
-synonym: "vector" RELATED [TyDI:58258]
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000543
-name: catfish pond
-is_a: OBT:000406 ! recreational fishing fish pond
-
-[Term]
-id: OBT:000544
-name: caulosphere
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000545
-name: caulosphere part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000546
-name: cellar
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000547
-name: cellulose
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000548
-name: cellulosic substrate
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000549
-name: cereal flours feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000550
-name: cerebrospinal fluid
-synonym: "cerebro-spinal fluid" EXACT [TyDI:57962]
-synonym: "CSF" EXACT [TyDI:57960]
-synonym: "liquor cerebrospinalis" EXACT [TyDI:57961]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000551
-name: cervix
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000552
-name: chained
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000553
-name: chair
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000554
-name: chapel
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000555
-name: chemotroph
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000556
-name: chest
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000557
-name: chyle
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000558
-name: chyme
-synonym: "chymus" EXACT [TyDI:57943]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000559
-name: circulatory system
-synonym: "cardiovascular system" EXACT [TyDI:57133]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000560
-name: clothe
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000561
-name: coal
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000562
-name: coast
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000563
-name: coccobacillus
-synonym: "oval-shaped" RELATED [TyDI:57691]
-synonym: "ovoid-shaped" RELATED [TyDI:57690]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000564
-name: cochlear prosthesis
-synonym: "cochlear implant" RELATED [TyDI:56520]
-is_a: OBT:003645 ! ocular prosthesis
-
-[Term]
-id: OBT:000565
-name: coelom fluid
-synonym: "coelomic fluid" EXACT [TyDI:57793]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000566
-name: coffeemaker
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000567
-name: cold seep
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000568
-name: combustible liquid
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000569
-name: common millet feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000570
-name: composite food
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000571
-name: compost
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:000572
-name: conjunctiva
-is_a: OBT:000277 ! eye part
-
-[Term]
-id: OBT:000573
-name: cornea
-is_a: OBT:000277 ! eye part
-
-[Term]
-id: OBT:000574
-name: cosmetics
-is_a: OBT:000316 ! household product
-
-[Term]
-id: OBT:000575
-name: countertop
-synonym: "worktop" RELATED [TyDI:57193]
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000576
-name: crabtree negative
-synonym: "crabtree-negative" EXACT [TyDI:50087]
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000577
-name: crabtree positive
-synonym: "crabtree-positive" EXACT [TyDI:50096]
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000578
-name: cuboidal
-synonym: "sarcina" RELATED [TyDI:50700]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000579
-name: culture system
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000580
-name: curtain
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000581
-name: cut
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000582
-name: cutting board
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000583
-name: dairy farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000584
-name: dairy starter culture
-synonym: "dairy starter" EXACT []
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000585
-name: dead matter
-synonym: "dead organic matter" RELATED [TyDI:50338]
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000586
-name: dead wood
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000587
-name: deep periodontal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000588
-name: deep sea
-synonym: "deep-sea" EXACT [TyDI:58017]
-synonym: "deep-sea environment" EXACT [TyDI:58016]
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000589
-name: deep tissue
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000590
-name: dental biofilm
-is_a: OBT:000313 ! host associated biofilm
-
-[Term]
-id: OBT:000591
-name: dental prosthesis
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000592
-name: desert
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000593
-name: desert soil
-synonym: "desert" RELATED [TyDI:57776]
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000594
-name: dishcloth
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000595
-name: dishwasher
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000596
-name: domestic animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000597
-name: drinking water facility
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000598
-name: drug resistant
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000599
-name: drug sensitive
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000600
-name: drug tolerant
-is_a: OBT:000381 ! phenotype wrt drug impact
-
-[Term]
-id: OBT:000601
-name: dune soil
-synonym: "dune" RELATED [TyDI:57158]
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000602
-name: ear
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000603
-name: ear canal
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000604
-name: ear wax
-synonym: "cerumen" EXACT [TyDI:57914]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000605
-name: earring hole
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000606
-name: earth
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000607
-name: eating and drinking place
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000608
-name: ectomycorrhizal fungus
-synonym: "ectomycorrhizal" RELATED [TyDI:57805]
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000609
-name: ectoparasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000610
-name: edible film
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000611
-name: effluent
-synonym: "industrial effluent" RELATED [TyDI:50516]
-is_a: OBT:000325 ! industrial water and effluent
-
-[Term]
-id: OBT:000612
-name: egg part
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000613
-name: embryonic structure
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000614
-name: encapsulated
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000615
-name: endometrium
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000616
-name: endoparasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000617
-name: endophyte
-synonym: "endophytic " EXACT [TyDI:55602]
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000618
-name: endozootic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000619
-name: epithelial layer
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000620
-name: epizootic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000621
-name: excavation
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000622
-name: excreta
-synonym: "excretion" EXACT [TyDI:57919]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000623
-name: extra-uterus
-synonym: "extra-uterine" RELATED [TyDI:50542]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000624
-name: extractive industrial site
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000625
-name: extreme high temperature environment
-is_a: OBT:000309 ! high temperature environment
-
-[Term]
-id: OBT:000626
-name: extremely acid environment
-is_a: OBT:000176 ! acid environment
-
-[Term]
-id: OBT:000627
-name: eye
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000628
-name: filament-shaped
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000629
-name: filamentous
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000630
-name: fish farm
-is_a: OBT:000336 ! mariculture farm
-
-[Term]
-id: OBT:000631
-name: fish meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000632
-name: fluffy colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000633
-name: food for particular diet
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000634
-name: forest soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000635
-name: free-living diazotroph
-is_a: OBT:000257 ! diazotroph
-
-[Term]
-id: OBT:000636
-name: freezer
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000637
-name: freshwater aquarium
-is_a: OBT:000198 ! aquarium
-
-[Term]
-id: OBT:000638
-name: gall bladder
-synonym: "gallblader" EXACT [TyDI:57800]
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000639
-name: garden soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000640
-name: gastric acid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000641
-name: gastrointestinal tract
-synonym: "alimentary canal" RELATED [TyDI:54495]
-synonym: "digestive tract" RELATED [TyDI:54492]
-synonym: "gastrointestinal" RELATED [TyDI:54493]
-synonym: "GI tract" EXACT [TyDI:54491]
-synonym: "GIT" EXACT [TyDI:54494]
-synonym: "intestinal region" RELATED [TyDI:53836]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000642
-name: gastrointestinal tract part
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000643
-name: genital tract
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000644
-name: gill
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000645
-name: gingival crevice
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000646
-name: gingival lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000647
-name: glial cell
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000648
-name: gram-negative
-synonym: "gram -" RELATED [TyDI:57829]
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000649
-name: gram-positive
-synonym: "gram +" RELATED [TyDI:57824]
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000650
-name: gram-variable
-is_a: OBT:000296 ! gram stain phenotype
-
-[Term]
-id: OBT:000651
-name: granite stone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000652
-name: grape-like clustered
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000653
-name: green forage
-is_a: OBT:000287 ! forage
-
-[Term]
-id: OBT:000654
-name: groin
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000655
-name: growing plant
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000656
-name: halophile
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:000657
-name: halophobe
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:000658
-name: handkerchief
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000659
-name: harbor
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000660
-name: harvesting tool
-is_a: OBT:000185 ! agricultural tool
-
-[Term]
-id: OBT:000661
-name: head kidney
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000662
-name: heart valve
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000663
-name: hemodialysis machine
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000664
-name: hemolymph
-synonym: "haemolymph" EXACT [TyDI:56832]
-is_a: OBT:000200 ! arthropod part
-
-[Term]
-id: OBT:000665
-name: heterotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000666
-name: high chair tray
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000667
-name: high salt concentration environment
-is_a: OBT:000302 ! haline environment
-
-[Term]
-id: OBT:000668
-name: highly acid environment
-is_a: OBT:000176 ! acid environment
-
-[Term]
-id: OBT:000669
-name: home drainage system
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000670
-name: home food processing equipment
-synonym: "domestic food processing equipment" EXACT [TyDI:55574]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000671
-name: home heating system
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000672
-name: hospital gown
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000673
-name: hospital hot water
-is_a: OBT:000312 ! hospital water
-
-[Term]
-id: OBT:000674
-name: hot spring biomat
-is_a: OBT:000213 ! biomat
-
-[Term]
-id: OBT:000675
-name: hotel
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000676
-name: hotel carpet
-is_a: OBT:000219 ! carpet
-
-[Term]
-id: OBT:000677
-name: household waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000678
-name: human body
-is_a: OBT:000214 ! body
-
-[Term]
-id: OBT:000679
-name: humus
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000680
-name: humus soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000681
-name: ice
-is_a: OBT:000238 ! cold temperature environment
-
-[Term]
-id: OBT:000682
-name: indoor air
-is_a: OBT:000186 ! air
-
-[Term]
-id: OBT:000683
-name: industrial building
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000684
-name: industrial equipment
-is_a: OBT:000324 ! industrial site
-
-[Term]
-id: OBT:000685
-name: industrial waste
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:000686
-name: innate immune system
-is_a: OBT:000321 ! immune system
-
-[Term]
-id: OBT:000687
-name: inner ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000688
-name: insect part
-is_a: OBT:000200 ! arthropod part
-
-[Term]
-id: OBT:000689
-name: interstitial fluid
-synonym: "intercellular fluid" EXACT [TyDI:57238]
-synonym: "tissue fluid" EXACT [TyDI:57239]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000690
-name: intertidal zone
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000691
-name: intestinal content
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000692
-name: intra-uterus
-synonym: "intra-uterine" RELATED [TyDI:50499]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000693
-name: intravascular catheter
-is_a: OBT:000223 ! catheter
-
-[Term]
-id: OBT:000694
-name: invertebrate species
-synonym: "invertebrate" RELATED [TyDI:57989]
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000695
-name: jail
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000696
-name: jungle
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000697
-name: kitchen
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000698
-name: kitchen sink
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000699
-name: kitchen sponge
-synonym: "dish sponge" RELATED [TyDI:52187]
-synonym: "dish-washing sponge" RELATED [TyDI:52188]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000700
-name: laboratory animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000701
-name: laryngeal prosthetic device
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000702
-name: latrine
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000703
-name: leafy soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000704
-name: lentic water
-synonym: "stagnant water" RELATED [TyDI:50521]
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000705
-name: lentic water body
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:000706
-name: leukocyte
-synonym: "leucocyte" EXACT [TyDI:57142]
-synonym: "white blood cell" EXACT [TyDI:57143]
-is_a: OBT:000320 ! immune cell
-
-[Term]
-id: OBT:000707
-name: lichen
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000708
-name: light organ
-synonym: "light-emitting organ" EXACT [TyDI:50411]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000709
-name: limestone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000710
-name: lining
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000711
-name: liquid food
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000712
-name: lithotroph
-is_a: OBT:000385 ! phenotype wrt reducing equivalent source
-
-[Term]
-id: OBT:000713
-name: lotic water body
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:000714
-name: lower respiratory tract
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000715
-name: lucerne
-is_a: OBT:000287 ! forage
-
-[Term]
-id: OBT:000716
-name: lung
-synonym: "pulmonary" RELATED [TyDI:54508]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000717
-name: lymph
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000718
-name: lymph node
-is_a: OBT:000334 ! lymphatic system part
-
-[Term]
-id: OBT:000719
-name: lymphatic system
-synonym: "lymphatic" RELATED [TyDI:50404]
-synonym: "lymphatics" EXACT [TyDI:50403]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000720
-name: maize feed
-synonym: "corn feed" NARROW []
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000721
-name: maize storage
-synonym: "corn storage" NARROW []
-is_a: OBT:000423 ! silo
-
-[Term]
-id: OBT:000722
-name: malt feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000723
-name: mammalian part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000724
-name: marine eukaryotic species
-is_a: OBT:000199 ! aquatic eukaryotic species
-
-[Term]
-id: OBT:000725
-name: marine freight transport equipment
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000726
-name: meat meal
-is_a: OBT:000340 ! meat and bone meal
-
-[Term]
-id: OBT:000727
-name: medical bed sheet
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000728
-name: medical glove
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000729
-name: medical mask
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000730
-name: animal membrane
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000731
-name: meninges
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000732
-name: metaphytic
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000733
-name: methanogenic
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000734
-name: methylotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000735
-name: microaerotolerant
-is_a: OBT:000183 ! aerotolerant
-
-[Term]
-id: OBT:000736
-name: microanaerobe
-is_a: OBT:000189 ! anaerobe
-
-[Term]
-id: OBT:000737
-name: microbial mat
-is_a: OBT:000213 ! biomat
-
-[Term]
-id: OBT:000738
-name: microwave oven
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000739
-name: mid-vaginal wall
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000740
-name: middle ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000741
-name: milking machine
-is_a: OBT:000250 ! dairy farm equipment
-
-[Term]
-id: OBT:000742
-name: mineral oil
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000743
-name: mineral soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000744
-name: mixotroph
-is_a: OBT:000379 ! phenotype wrt carbon source
-
-[Term]
-id: OBT:000745
-name: moss
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000746
-name: mound
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000747
-name: mountain
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000748
-name: muddy water
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000749
-name: mural painting
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000750
-name: musculoskeletal system
-synonym: "locomotor apparatus" RELATED [TyDI:51092]
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000751
-name: musculoskeletal system part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:000752
-name: mushroom
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:000753
-name: mussel farm
-is_a: OBT:000336 ! mariculture farm
-
-[Term]
-id: OBT:000754
-name: nare
-synonym: "nostril" RELATED [TyDI:56380]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000755
-name: nasal cavity
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000756
-name: nasal epithelia
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000757
-name: nasopharynx
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000758
-name: natron-alkaliphilic
-is_a: OBT:000188 ! alkaliphile
-
-[Term]
-id: OBT:000759
-name: natural gas
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000760
-name: necropolis
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000761
-name: necrotic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000762
-name: necrotrophic
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000763
-name: negative aerotactic
-is_a: OBT:000182 ! aerotactic
-
-[Term]
-id: OBT:000764
-name: negative chemotactic
-is_a: OBT:000230 ! chemotactic
-
-[Term]
-id: OBT:000765
-name: nerve
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000766
-name: nervous system
-synonym: "neurologic" EXACT [TyDI:57094]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000767
-name: nose
-synonym: "nasal" RELATED [TyDI:54437]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000768
-name: noxious plant
-is_a: OBT:000184 ! agricultural pest
-
-[Term]
-id: OBT:000769
-name: obligate aerobe
-is_a: OBT:000179 ! aerobe
-
-[Term]
-id: OBT:000770
-name: obligate anaerobe
-is_a: OBT:000189 ! anaerobe
-
-[Term]
-id: OBT:000771
-name: obligate parasite
-is_a: OBT:000372 ! parasite
-
-[Term]
-id: OBT:000772
-name: obligate piezophile
-synonym: "obligate barophile " EXACT [TyDI:54212]
-is_a: OBT:000390 ! piezophile
-
-[Term]
-id: OBT:000773
-name: office
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000774
-name: oil tanker
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000775
-name: open-ocean
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000776
-name: opportunistic pathogen
-synonym: "opportunist" EXACT [TyDI:54918]
-is_a: OBT:000375 ! pathogen
-
-[Term]
-id: OBT:000777
-name: organic waste
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000778
-name: organotroph
-is_a: OBT:000385 ! phenotype wrt reducing equivalent source
-
-[Term]
-id: OBT:000779
-name: ornithogenic soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000780
-name: osteolytic bone lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000781
-name: outdoor air
-is_a: OBT:000186 ! air
-
-[Term]
-id: OBT:000782
-name: outer ear
-is_a: OBT:000264 ! ear part
-
-[Term]
-id: OBT:000783
-name: ovary
-synonym: "ovaries" RELATED [TyDI:56007]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000784
-name: oxidase negative
-is_a: OBT:000371 ! oxidase activity
-
-[Term]
-id: OBT:000785
-name: oxidase positive
-is_a: OBT:000371 ! oxidase activity
-
-[Term]
-id: OBT:000786
-name: pacemaker
-is_a: OBT:003632 ! prosthetic cardiac device
-
-[Term]
-id: OBT:000787
-name: packaging
-is_a: OBT:000434 ! storage equipment
-
-[Term]
-id: OBT:000788
-name: packed lunch
-synonym: "bag lunch" RELATED [TyDI:58085]
-synonym: "box lunch" RELATED [TyDI:58087]
-synonym: "pack lunch" RELATED [TyDI:58088]
-synonym: "sack lunch" RELATED [TyDI:58086]
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000789
-name: paired
-synonym: "diplobacilli" RELATED [TyDI:50739]
-synonym: "diplococci" RELATED [TyDI:50738]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000790
-name: pancreas
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000791
-name: pancreatic duct
-is_a: OBT:000258 ! digestive system part
-
-[Term]
-id: OBT:000792
-name: paper
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000793
-name: paper carton
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000794
-name: paper pulp
-is_a: OBT:000323 ! industrial product
-
-[Term]
-id: OBT:000795
-name: passenger train
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000796
-name: perchlorate-contaminated site
-is_a: OBT:000244 ! contaminated site
-
-[Term]
-id: OBT:000797
-name: periodontal lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000798
-name: periphytic
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000799
-name: peritoneal fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000800
-name: pest insect
-is_a: OBT:000184 ! agricultural pest
-
-[Term]
-id: OBT:000801
-name: phagocyte
-is_a: OBT:000320 ! immune cell
-
-[Term]
-id: OBT:000802
-name: pharyngeal mucosa
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000803
-name: phenol
-is_a: OBT:000322 ! industrial chemical
-
-[Term]
-id: OBT:000804
-name: photosynthetic
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000805
-name: phototroph
-is_a: OBT:000383 ! phenotype wrt living energy source
-
-[Term]
-id: OBT:000806
-name: phylloplane
-is_a: OBT:000389 ! phyllosphere part
-
-[Term]
-id: OBT:000807
-name: phylloplane part
-is_a: OBT:000388 ! phyllosphere
-
-[Term]
-id: OBT:000808
-name: pig farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000809
-name: pigmented
-is_a: OBT:000380 ! phenotype wrt color
-
-[Term]
-id: OBT:000810
-name: pillow as equipment
-is_a: OBT:000210 ! bedroom equipment
-
-[Term]
-id: OBT:000811
-name: placenta
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000812
-name: plant nodule
-is_a: OBT:000442 ! symbiosome
-
-[Term]
-id: OBT:000813
-name: plant opportunist
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:000814
-name: plant organ
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000815
-name: plant product and primary derivative thereof
-synonym: "food processing plant" RELATED [TyDI:49608]
-synonym: "plant-derived foodstuff" RELATED [TyDI:56002]
-is_a: OBT:000240 ! commodity and primary derivative thereof
-
-[Term]
-id: OBT:000816
-name: plant tissue
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000817
-name: pleomorphic
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000818
-name: pleural fluid
-synonym: "pleural effusion" RELATED [TyDI:57940]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000819
-name: pneumonic lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000820
-name: porifera
-is_a: OBT:000199 ! aquatic eukaryotic species
-
-[Term]
-id: OBT:000821
-name: positive aerotactic
-is_a: OBT:000182 ! aerotactic
-
-[Term]
-id: OBT:000822
-name: positive chemotactic
-is_a: OBT:000230 ! chemotactic
-
-[Term]
-id: OBT:000823
-name: potluck
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000824
-name: poultry farm
-is_a: OBT:000194 ! animal farm
-
-[Term]
-id: OBT:000825
-name: prepuce
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000826
-name: probe
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000827
-name: probiotic
-is_a: OBT:000195 ! animal hosted
-
-[Term]
-id: OBT:000828
-name: processed commodity and food
-is_a: OBT:000397 ! prepared food
-
-[Term]
-id: OBT:000829
-name: prostate
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000830
-name: prosthetic joint
-synonym: "joint prosthesis" EXACT []
-is_a: OBT:000398 ! prosthesis
-
-[Term]
-id: OBT:000831
-name: pus
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000832
-name: quinoa feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000833
-name: rash
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000834
-name: raw primary commodities
-synonym: "raw food" RELATED [TyDI:57190]
-synonym: "uncooked food" RELATED [TyDI:57189]
-synonym: "unprocessed food" RELATED [TyDI:57187]
-synonym: "untreated food" RELATED [TyDI:57188]
-is_a: OBT:000397 ! prepared food
-
-[Term]
-id: OBT:000835
-name: ready made meal
-synonym: "prepackaged meal" RELATED [TyDI:58097]
-synonym: "ready meal" RELATED [TyDI:58098]
-synonym: "ready to eat meal" RELATED [TyDI:58100]
-synonym: "TV dinner" RELATED [TyDI:58099]
-is_a: OBT:000339 ! meal
-
-[Term]
-id: OBT:000836
-name: reef surface biofilm
-is_a: OBT:000212 ! biofilm in natural environment
-
-[Term]
-id: OBT:000837
-name: refrigerator
-synonym: "fridge" RELATED [TyDI:57118]
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000838
-name: research and study center
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000839
-name: residential carpet
-is_a: OBT:000219 ! carpet
-
-[Term]
-id: OBT:000840
-name: residential toilet
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000841
-name: respiratory therapy equipment
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000842
-name: rice feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000843
-name: road
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000844
-name: road junction
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000845
-name: road side
-is_a: OBT:000412 ! road part
-
-[Term]
-id: OBT:000846
-name: rock
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000847
-name: rock scraping
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000848
-name: rod-shaped
-synonym: "bacilliform" EXACT [TyDI:57694]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000849
-name: root part
-is_a: OBT:000411 ! rhizosphere part
-
-[Term]
-id: OBT:000850
-name: round-shaped
-synonym: "coccus" RELATED [TyDI:57763]
-synonym: "sphere-shaped" RELATED [TyDI:57762]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000851
-name: rye feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000852
-name: salt crust
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000853
-name: sandstone
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000854
-name: sandstone monument
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000855
-name: sandy soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000856
-name: sauna
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000857
-name: savannah
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000858
-name: school
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000859
-name: school bus
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000860
-name: scratch
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000861
-name: scrub as clothing
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000862
-name: seabed
-synonym: "sea floor" EXACT [TyDI:54745]
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:000863
-name: secretion
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000864
-name: sensor
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000865
-name: sheathed
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000866
-name: ship ballast
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000867
-name: ship ballast water
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000868
-name: ship tank
-is_a: OBT:000289 ! freight transport equipment
-
-[Term]
-id: OBT:000869
-name: shower
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000870
-name: shrimp hatchery
-is_a: OBT:000303 ! hatchery
-
-[Term]
-id: OBT:000871
-name: silage
-is_a: OBT:000365 ! organic matter
-
-[Term]
-id: OBT:000872
-name: singled
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000873
-name: sink drain
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000874
-name: site contaminated with organic compound
-is_a: OBT:000244 ! contaminated site
-
-[Term]
-id: OBT:000875
-name: skin
-synonym: "cutaneous" RELATED [TyDI:54464]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000876
-name: skin bump
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000877
-name: skin nodule
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000878
-name: skin papule
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:000879
-name: small colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000880
-name: smooth colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000881
-name: snow
-is_a: OBT:000238 ! cold temperature environment
-
-[Term]
-id: OBT:000882
-name: sofa as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000883
-name: soft tissue
-is_a: OBT:000196 ! animal tissue
-
-[Term]
-id: OBT:000884
-name: soil crust
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000885
-name: soil matter
-is_a: OBT:000428 ! soil part
-
-[Term]
-id: OBT:000886
-name: sorghum feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000887
-name: spinal cord
-is_a: OBT:000357 ! nervous system part
-
-[Term]
-id: OBT:000888
-name: spiral-shaped
-synonym: "helical" RELATED [TyDI:57757]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000889
-name: spirometer
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000890
-name: spleen
-synonym: "splenic" EXACT [TyDI:51044]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000891
-name: square-shaped
-synonym: "cube-like-shaped" RELATED [TyDI:57732]
-synonym: "cuboidal" RELATED [TyDI:50699]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000892
-name: stalked
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000893
-name: star-shaped
-synonym: "rosette-like" RELATED [TyDI:57738]
-synonym: "star-like" RELATED [TyDI:57737]
-is_a: OBT:000228 ! cellular shape phenotype
-
-[Term]
-id: OBT:000894
-name: starter yeast
-synonym: "commercial starter" EXACT [TyDI:50918]
-synonym: "commercial yeast" EXACT [TyDI:50920]
-synonym: "yeast starter" EXACT [TyDI:50919]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000895
-name: stomach content
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000896
-name: stool as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000897
-name: structured colony
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:000898
-name: subgingival biofilm
-is_a: OBT:000313 ! host associated biofilm
-
-[Term]
-id: OBT:000899
-name: subway
-synonym: "metro" RELATED [TyDI:56961]
-synonym: "metropolitan" RELATED [TyDI:56960]
-is_a: OBT:000405 ! public transport
-
-[Term]
-id: OBT:000900
-name: sulfide-oxidizing bioreactor
-is_a: OBT:000180 ! aerobic bioreactor
-
-[Term]
-id: OBT:000901
-name: sulfidogenic bioreactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000902
-name: surface of food
-is_a: OBT:000373 ! part of food
-
-[Term]
-id: OBT:000903
-name: surface soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000904
-name: surface water
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:000905
-name: surgical cap
-synonym: "scrub cap" RELATED [TyDI:57233]
-is_a: OBT:000341 ! medical outfit
-
-[Term]
-id: OBT:000906
-name: symbiotic diazotroph
-is_a: OBT:000257 ! diazotroph
-
-[Term]
-id: OBT:000907
-name: synovial fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000908
-name: table as furniture
-is_a: OBT:000291 ! furniture
-
-[Term]
-id: OBT:000909
-name: tableware
-synonym: "dishware" RELATED [TyDI:57196]
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000910
-name: tap
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000911
-name: terminal airway
-synonym: "airway" RELATED [TyDI:57983]
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000912
-name: terrestrial plant
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:000913
-name: testis
-synonym: "testes" EXACT [TyDI:57109]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000914
-name: tetrad
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000915
-name: therapeutic ultrasound equipment
-is_a: OBT:000448 ! therapeutic equipment
-
-[Term]
-id: OBT:000916
-name: thermometer as medical device
-synonym: "<new synonym>" RELATED [TyDI:57022]
-synonym: "clinical thermometer" RELATED [TyDI:57023]
-synonym: "hospital thermometer" RELATED [TyDI:57024]
-is_a: OBT:000256 ! diagnostic equipment
-
-[Term]
-id: OBT:000917
-name: thermophilic anaerobic methanogenic reactor
-is_a: OBT:000190 ! anaerobic bioreactor
-
-[Term]
-id: OBT:000918
-name: throat
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000919
-name: throat swab
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000920
-name: toilet
-is_a: OBT:000414 ! room
-
-[Term]
-id: OBT:000921
-name: toilet bowl
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000922
-name: toilet seat
-is_a: OBT:000455 ! toilet equipment
-
-[Term]
-id: OBT:000923
-name: toiletries
-is_a: OBT:000316 ! household product
-
-[Term]
-id: OBT:000924
-name: tomb
-is_a: OBT:000352 ! monument
-
-[Term]
-id: OBT:000925
-name: toundra
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000926
-name: towel
-is_a: OBT:000447 ! textile
-
-[Term]
-id: OBT:000927
-name: tree part
-is_a: OBT:000395 ! plant part
-
-[Term]
-id: OBT:000928
-name: trichome forming
-synonym: "trichome-forming" EXACT [TyDI:57617]
-is_a: OBT:000353 ! multicellular arrangement phenotype
-
-[Term]
-id: OBT:000929
-name: trona crust
-synonym: "kaum crust" EXACT [TyDI:56987]
-is_a: OBT:000350 ! mineral matter
-
-[Term]
-id: OBT:000930
-name: tropical country
-is_a: OBT:000458 ! tropical zone
-
-[Term]
-id: OBT:000931
-name: trypanosome
-is_a: OBT:000400 ! protozoa
-
-[Term]
-id: OBT:000932
-name: tuberculoid granuloma
-is_a: OBT:000298 ! granuloma
-
-[Term]
-id: OBT:000933
-name: ulcer
-synonym: "ulceration" RELATED [TyDI:50416]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000934
-name: ulcerative lesion
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000935
-name: upland
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000936
-name: upper respiratory tract
-is_a: OBT:000408 ! respiratory tract part
-
-[Term]
-id: OBT:000937
-name: ureter
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000938
-name: urethra
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000939
-name: urinary catheter
-is_a: OBT:000223 ! catheter
-
-[Term]
-id: OBT:000940
-name: urinary tract
-synonym: "urinary" RELATED [TyDI:50526]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000941
-name: urogenital tract
-synonym: "urogenital" RELATED [TyDI:56017]
-synonym: "urogenital area" RELATED [TyDI:56018]
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:000942
-name: uterus
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000943
-name: vagina
-synonym: "vaginal" RELATED [TyDI:50358]
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:000944
-name: valley
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000945
-name: vascular
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:000946
-name: vertebrate
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000947
-name: veterinary drug
-is_a: OBT:003680 ! veterinary product
-
-[Term]
-id: OBT:000948
-name: vitreous fluid
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000949
-name: vitreous humor
-synonym: "vitreous body" EXACT [TyDI:57966]
-synonym: "vitreous humour" EXACT [TyDI:57965]
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000950
-name: volcanic soil
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:000951
-name: volcano
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000952
-name: vomit
-is_a: OBT:000215 ! body fluid
-
-[Term]
-id: OBT:000953
-name: washbasin
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:000954
-name: washing machine
-is_a: OBT:000260 ! domestic appliance
-
-[Term]
-id: OBT:000955
-name: water cooling system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000956
-name: water droplet
-is_a: OBT:000468 ! water
-
-[Term]
-id: OBT:000957
-name: water from air and water system
-is_a: OBT:000325 ! industrial water and effluent
-
-[Term]
-id: OBT:000958
-name: water heater system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000959
-name: water storage system
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000960
-name: water transport structure
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000961
-name: water treatment plant
-synonym: "water treatment facility" RELATED [TyDI:54688]
-is_a: OBT:000201 ! artificial water structure
-
-[Term]
-id: OBT:000962
-name: water vapor
-is_a: OBT:000468 ! water
-
-[Term]
-id: OBT:000963
-name: welfare center
-is_a: OBT:000403 ! public building
-
-[Term]
-id: OBT:000964
-name: wetland
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000965
-name: wheat feed
-is_a: OBT:000229 ! cereal feed
-
-[Term]
-id: OBT:000966
-name: whirlpool bath
-is_a: OBT:000208 ! bathroom equipment
-
-[Term]
-id: OBT:000967
-name: wild animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000968
-name: wine yeast
-synonym: "oenological yeast" EXACT [TyDI:50875]
-is_a: OBT:000432 ! starter culture
-
-[Term]
-id: OBT:000969
-name: woody landscape
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:000970
-name: wound
-synonym: "injury" EXACT [TyDI:50484]
-is_a: OBT:000332 ! lesion
-
-[Term]
-id: OBT:000971
-name: zoo animal
-is_a: OBT:000193 ! animal
-
-[Term]
-id: OBT:000972
-name: Asteraceae
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:000973
-name: Cerrado
-is_a: OBT:000857 ! savannah
-
-[Term]
-id: OBT:000974
-name: Crassulaceae
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:000975
-name: PCE contaminated site
-synonym: "perchloroethylene contaminated site" EXACT [TyDI:50826]
-synonym: "tetrachloroethene contaminated site" EXACT [TyDI:50825]
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:000976
-name: Tasmanian devil
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:000977
-name: abalone
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:000978
-name: agranulocyte
-is_a: OBT:000706 ! leukocyte
-
-[Term]
-id: OBT:000979
-name: air conditioning system
-synonym: "air conditioner" EXACT [TyDI:53043]
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:000980
-name: air filter
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:000981
-name: ale yeast
-synonym: "ale brewer's yeast" EXACT [TyDI:50884]
-is_a: OBT:000511 ! beer yeast
-
-[Term]
-id: OBT:000982
-name: alfalfa silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:000983
-name: alkaline salt crust
-is_a: OBT:000852 ! salt crust
-
-[Term]
-id: OBT:000984
-name: animal based juice
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:000985
-name: animal waste
-is_a: OBT:000777 ! organic waste
-
-[Term]
-id: OBT:000986
-name: animal with life stage property
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:000987
-name: annelid
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:000988
-name: anus
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:000989
-name: arachnid
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:000990
-name: artery
-is_a: OBT:000525 ! blood vessel
-
-[Term]
-id: OBT:000991
-name: artic valley
-is_a: OBT:000944 ! valley
-
-[Term]
-id: OBT:000992
-name: ascidian
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:000993
-name: ash dump
-synonym: "ash dump site" EXACT [TyDI:50465]
-synonym: "ash dumping site" EXACT [TyDI:50466]
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:000994
-name: baby diaper
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:000995
-name: baby wipe
-synonym: "moist towel" RELATED [TyDI:56846]
-synonym: "wet towel" RELATED [TyDI:56847]
-synonym: "wet wipe" RELATED [TyDI:56848]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:000996
-name: backswamp
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:000997
-name: backwater
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:000998
-name: bacteriome
-is_a: OBT:000688 ! insect part
-
-[Term]
-id: OBT:000999
-name: baking powder
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001000
-name: baking soda
-synonym: "sodium bicarbonate" EXACT [TyDI:50899]
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001001
-name: bamboo
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001002
-name: bark
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001003
-name: barrier flat
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001004
-name: benzene-contaminated site
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:001005
-name: biofilm phenotype
-is_a: OBT:000015 ! phenotype wrt adhesion
-is_a: OBT:000016 ! phenotype wrt community behaviour
-
-[Term]
-id: OBT:001006
-name: bird and reptile GIT part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001007
-name: black pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001008
-name: blue pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001009
-name: bog
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001010
-name: boiler
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001011
-name: bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001012
-name: bone caries
-is_a: OBT:000538 ! caries
-
-[Term]
-id: OBT:001013
-name: botanical garden soil
-is_a: OBT:000639 ! garden soil
-
-[Term]
-id: OBT:001014
-name: brain abcess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001015
-name: branch
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001016
-name: brasserie
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001017
-name: breast
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001018
-name: breast milk
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001019
-name: brown pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001020
-name: buccal
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001021
-name: bulbous plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001022
-name: cafeteria
-synonym: "canteen" RELATED [TyDI:58190]
-synonym: "dining hall" RELATED [TyDI:58191]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001023
-name: café
-synonym: "coffee shop" RELATED [TyDI:58107]
-synonym: "coffeehouse" RELATED [TyDI:58106]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001024
-name: calcereous rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001025
-name: calorifier
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001026
-name: canopy humus
-is_a: OBT:000679 ! humus
-
-[Term]
-id: OBT:001027
-name: cargo oil tank
-is_a: OBT:000868 ! ship tank
-
-[Term]
-id: OBT:001028
-name: central nervous system
-is_a: OBT:000766 ! nervous system
-
-[Term]
-id: OBT:001029
-name: cereal and pseudo-cereal dough-based product
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001030
-name: cheese starter culture
-is_a: OBT:000584 ! dairy starter culture
-
-[Term]
-id: OBT:001031
-name: chemical plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001032
-name: chewing stick
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001033
-name: chipboard factory
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001034
-name: chlorine-contaminated site
-is_a: OBT:000874 ! site contaminated with organic compound
-
-[Term]
-id: OBT:001035
-name: chlorophototroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:001036
-name: chocolate product
-synonym: "chocolate" RELATED [TyDI:50114]
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001037
-name: clay
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001038
-name: clean room
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001039
-name: coal spoil
-synonym: "coal residue" RELATED [TyDI:49847]
-is_a: OBT:000561 ! coal
-
-[Term]
-id: OBT:001040
-name: coastal fish farm
-is_a: OBT:000630 ! fish farm
-
-[Term]
-id: OBT:001041
-name: coastal wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001042
-name: college
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001043
-name: comma-shaped
-synonym: "comma shaped" EXACT [TyDI:57744]
-synonym: "vibrio-shaped" RELATED [TyDI:57743]
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001044
-name: condiment
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001045
-name: confectionery
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001046
-name: cooling tower
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001047
-name: cooling water
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001048
-name: coral
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001049
-name: corneal ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001050
-name: cortex
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001051
-name: cortical bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001052
-name: cotton swab
-synonym: "cotton bud" RELATED [TyDI:56786]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001053
-name: cotton-waste compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001054
-name: cream pigmented
-synonym: "beige pigmented" RELATED [TyDI:56779]
-synonym: "creamy white pigmented" RELATED [TyDI:56778]
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001055
-name: creek
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001056
-name: creosol
-is_a: OBT:000803 ! phenol
-
-[Term]
-id: OBT:001057
-name: crucifer
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001058
-name: crude oil
-synonym: "fossil fuel" RELATED [TyDI:55651]
-synonym: "petroleum" EXACT [TyDI:55652]
-is_a: OBT:000742 ! mineral oil
-
-[Term]
-id: OBT:001059
-name: crustacean
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:001060
-name: cuticle
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001061
-name: cyanobacterial mat
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:001062
-name: dairy farming waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001063
-name: dead organism
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001064
-name: dead tissue
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001065
-name: decaying matter
-synonym: "decaying organic matter" RELATED [TyDI:51801]
-synonym: "saprophyte" RELATED [TyDI:51800]
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001066
-name: defrosted food
-synonym: " thawed food" EXACT [TyDI:55720]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001067
-name: dental abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001068
-name: dental caries
-synonym: "dental cavity" EXACT [TyDI:49761]
-synonym: "tooth decay" RELATED [TyDI:49760]
-is_a: OBT:000538 ! caries
-
-[Term]
-id: OBT:001069
-name: desert rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001070
-name: dietary supplement
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001071
-name: dining car
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001072
-name: dinner plate
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001073
-name: dish
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001074
-name: district heating plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001075
-name: drainage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001076
-name: drainage canal
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001077
-name: drainage ditch
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001078
-name: drink
-synonym: "beverage" EXACT [TyDI:50020]
-is_a: OBT:000711 ! liquid food
-
-[Term]
-id: OBT:001079
-name: drinking glass
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001080
-name: drinking water filter
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001081
-name: drinking water reservoir
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001082
-name: drinking water supply
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001083
-name: ear thermometer
-synonym: "tympanic thermometer" RELATED [TyDI:56942]
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001084
-name: eating utensil
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001085
-name: eel farm
-is_a: OBT:000630 ! fish farm
-
-[Term]
-id: OBT:001086
-name: egg and egg product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001087
-name: empyema
-is_a: OBT:000831 ! pus
-
-[Term]
-id: OBT:001088
-name: endodermis
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001089
-name: epidermis
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001090
-name: epidermis part
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001091
-name: epithelium
-synonym: "epithelial" RELATED [TyDI:49861]
-is_a: OBT:000619 ! epithelial layer
-
-[Term]
-id: OBT:001092
-name: estuary
-is_a: OBT:000690 ! intertidal zone
-
-[Term]
-id: OBT:001093
-name: evaporator
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001094
-name: extractive industry equipment
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001095
-name: extreme halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001096
-name: facial tissue
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001097
-name: factory
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001098
-name: facultative chemo lithotroph
-synonym: "facultative chemolithotroph " EXACT [TyDI:54393]
-is_a: OBT:000555 ! chemotroph
-
-[Term]
-id: OBT:001099
-name: fast food restaurant
-synonym: " quick service restaurant" RELATED [TyDI:58177]
-synonym: "fast-food restaurant" RELATED [TyDI:58176]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001100
-name: fat body
-is_a: OBT:000688 ! insect part
-
-[Term]
-id: OBT:001101
-name: feather pillow
-is_a: OBT:000810 ! pillow as equipment
-
-[Term]
-id: OBT:001102
-name: feces
-synonym: "dropping" RELATED [TyDI:52876]
-synonym: "dung" EXACT [TyDI:52875]
-synonym: "faecal" RELATED [TyDI:52880]
-synonym: "faeces" EXACT [TyDI:52874]
-synonym: "frass" RELATED [TyDI:52879]
-synonym: "pellet" RELATED [TyDI:52877]
-synonym: "stool" RELATED [TyDI:52878]
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001103
-name: female animal
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:001104
-name: fen
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001105
-name: fermentative
-synonym: "fermentation ability" EXACT [TyDI:56867]
-synonym: "fermentation capacity" EXACT [TyDI:56866]
-is_a: OBT:000665 ! heterotroph
-
-[Term]
-id: OBT:001106
-name: flower part
-is_a: OBT:000494 ! anthosphere part
-
-[Term]
-id: OBT:001107
-name: fluorescent pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001108
-name: food booth
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001109
-name: food cart
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001110
-name: food container
-synonym: "food package" RELATED []
-synonym: "food wrapping" RELATED []
-is_a: OBT:000787 ! packaging
-
-[Term]
-id: OBT:001111
-name: food flavour
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001112
-name: food processing appliance
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001113
-name: food processing effluent
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001114
-name: food rind
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001115
-name: food truck
-synonym: "food-vending vehicle" RELATED [TyDI:58180]
-synonym: "lunch truck" RELATED [TyDI:58181]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001116
-name: foot
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001117
-name: foregut
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001118
-name: forehead thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001119
-name: forest
-is_a: OBT:000969 ! woody landscape
-
-[Term]
-id: OBT:001120
-name: forest humus
-is_a: OBT:000679 ! humus
-
-[Term]
-id: OBT:001121
-name: freshwater wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001122
-name: fruit and primary derivative thereof
-synonym: "fruit" RELATED [TyDI:51591]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001123
-name: fruit part
-is_a: OBT:000541 ! carposphere part
-
-[Term]
-id: OBT:001124
-name: furuncle fluid
-is_a: OBT:000831 ! pus
-
-[Term]
-id: OBT:001125
-name: garden plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001126
-name: garden vegetable and primary derivative thereof
-synonym: "vegetable" RELATED [TyDI:51704]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001127
-name: gas seep
-is_a: OBT:000759 ! natural gas
-
-[Term]
-id: OBT:001128
-name: gastric antrum
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001129
-name: gastric body
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001130
-name: gelatine as ingredient
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001131
-name: golden pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001132
-name: grain and primary derivative thereof
-synonym: "oilseed" RELATED [TyDI:51242]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001133
-name: granitic rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001134
-name: granulocyte
-is_a: OBT:000706 ! leukocyte
-
-[Term]
-id: OBT:001135
-name: grass plant
-synonym: "grass" EXACT [TyDI:49773]
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001136
-name: grass silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001137
-name: green pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001138
-name: ground food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001139
-name: guar gum
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001140
-name: gut
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001141
-name: hairspray
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001142
-name: head
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001143
-name: hindgut
-synonym: "hind-gut" RELATED [TyDI:50111]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001144
-name: hip bone
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001145
-name: home-made food
-synonym: "home-prepared food" RELATED [TyDI:51032]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001146
-name: honey and apiculture product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001147
-name: hoof
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001148
-name: horticultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001149
-name: hot water tank
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001150
-name: hotel bathroom
-is_a: OBT:000502 ! bathroom
-
-[Term]
-id: OBT:001151
-name: human Bartholin abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001152
-name: human appendix abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001153
-name: humidifier
-is_a: OBT:000479 ! air treatment unit
-
-[Term]
-id: OBT:001154
-name: hypersaline microbial mat
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:001155
-name: incontinence pad
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001156
-name: indigo pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001157
-name: industrial organic waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001158
-name: industrial scrap
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001159
-name: industrial sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001160
-name: indwelling urinary catheter
-is_a: OBT:000939 ! urinary catheter
-
-[Term]
-id: OBT:001161
-name: infant formula
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001162
-name: ingredient for hot drink
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001163
-name: insect
-synonym: "insect host" RELATED [TyDI:51900]
-is_a: OBT:000496 ! arthropod
-
-[Term]
-id: OBT:001164
-name: irrigation ditch
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001165
-name: jellyfish
-synonym: "sea jelly" RELATED [TyDI:52321]
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001166
-name: joint
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001167
-name: kerosene
-is_a: OBT:000568 ! combustible liquid
-
-[Term]
-id: OBT:001168
-name: kitchen garbage
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001169
-name: laboratory
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001170
-name: lager yeast
-synonym: "lager brewer's yeast" EXACT [TyDI:50892]
-synonym: "lager-brewing yeast" EXACT [TyDI:50891]
-is_a: OBT:000511 ! beer yeast
-
-[Term]
-id: OBT:001171
-name: lake
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:001172
-name: landfill site waste
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001173
-name: leachate
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001174
-name: leaf
-synonym: "plant leaf" EXACT [TyDI:51761]
-is_a: OBT:000807 ! phylloplane part
-
-[Term]
-id: OBT:001175
-name: leaf part
-is_a: OBT:000807 ! phylloplane part
-
-[Term]
-id: OBT:001176
-name: leg
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001177
-name: legume seed and primary derivative thereof
-synonym: "legume" RELATED [TyDI:50093]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001178
-name: lenticel
-is_a: OBT:000545 ! caulosphere part
-
-[Term]
-id: OBT:001179
-name: leopard
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001180
-name: lignocellulose
-is_a: OBT:000547 ! cellulose
-
-[Term]
-id: OBT:001181
-name: liquid agricultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001182
-name: liver abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001183
-name: livestock habitat
-is_a: OBT:000003 ! animal habitat
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-
-[Term]
-id: OBT:001184
-name: lower gastrointestinal tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001185
-name: lumber
-is_a: OBT:000586 ! dead wood
-
-[Term]
-id: OBT:001186
-name: lunch box
-is_a: OBT:000909 ! tableware
-
-[Term]
-id: OBT:001187
-name: lynx
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001188
-name: lyophilized milk starter
-is_a: OBT:000584 ! dairy starter culture
-
-[Term]
-id: OBT:001189
-name: machinery
-synonym: "machine" RELATED [TyDI:49876]
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001190
-name: maize silage
-synonym: "corn silage" NARROW []
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001191
-name: malachite green effluent
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001192
-name: male animal
-synonym: "male" EXACT [TyDI:49873]
-is_a: OBT:000490 ! animal with age or sex property
-
-[Term]
-id: OBT:001193
-name: mammary gland
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001194
-name: manure compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001195
-name: marine coast
-synonym: "coastal marine environment" EXACT [TyDI:49836]
-is_a: OBT:000562 ! coast
-
-[Term]
-id: OBT:001196
-name: marine rock
-is_a: OBT:000846 ! rock
-
-[Term]
-id: OBT:001197
-name: maroon pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001198
-name: marsh
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001199
-name: mashed food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001200
-name: meat and meat product
-synonym: "animal meat" EXACT [TyDI:52959]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001201
-name: meristem
-synonym: "meristemic" RELATED [TyDI:49807]
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001202
-name: mesentery
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001203
-name: meso-halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001204
-name: methanol oxidizing
-is_a: OBT:000734 ! methylotroph
-
-[Term]
-id: OBT:001205
-name: methanotroph
-synonym: "methane-oxidizing " EXACT [TyDI:54831]
-synonym: "methanophile " EXACT [TyDI:54830]
-synonym: "methanotrophic " RELATED [TyDI:54829]
-is_a: OBT:000734 ! methylotroph
-
-[Term]
-id: OBT:001206
-name: midge
-is_a: OBT:000800 ! pest insect
-
-[Term]
-id: OBT:001207
-name: midgut
-synonym: "embryonic digestive tube" RELATED [TyDI:55725]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001208
-name: milk and milk product
-synonym: "dairy product" RELATED [TyDI:49802]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001209
-name: milled food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001210
-name: mine
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001211
-name: mine drainage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001212
-name: mine waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001213
-name: model plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001214
-name: moderate halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001215
-name: mollusc
-synonym: "mollusca" RELATED [TyDI:55717]
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001216
-name: moor
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001217
-name: mouth part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001218
-name: mucosal tissue
-synonym: "mucosa" RELATED [TyDI:51869]
-is_a: OBT:000710 ! lining
-
-[Term]
-id: OBT:001219
-name: mucous membrane
-synonym: "mucus membrane" EXACT [TyDI:55642]
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001220
-name: mucus
-synonym: "mucous" RELATED [TyDI:49731]
-synonym: "mucous flow" RELATED [TyDI:49730]
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001221
-name: mud
-synonym: "ooze" RELATED [TyDI:51894]
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001222
-name: mud volcano
-is_a: OBT:000951 ! volcano
-
-[Term]
-id: OBT:001223
-name: mudpit
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001224
-name: municipal sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001225
-name: municipal solid waste
-is_a: OBT:000677 ! household waste
-
-[Term]
-id: OBT:001226
-name: muscle
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001227
-name: nasal passage abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001228
-name: nasal secretion
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001229
-name: neck
-synonym: "cervical" RELATED [TyDI:50053]
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001230
-name: nematode
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001231
-name: nursing home
-is_a: OBT:000963 ! welfare center
-
-[Term]
-id: OBT:001232
-name: nut and primary derivative thereof
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001233
-name: obligate halophile
-is_a: OBT:000656 ! halophile
-
-[Term]
-id: OBT:001234
-name: offal and product thereof
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001235
-name: oil field
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001236
-name: oil industry
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001237
-name: oil well
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001238
-name: oilfruit and primary derivative thereof
-is_a: OBT:000815 ! plant product and primary derivative thereof
-
-[Term]
-id: OBT:001239
-name: oral thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001240
-name: orange pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001241
-name: oven
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001242
-name: panda
-is_a: OBT:000971 ! zoo animal
-
-[Term]
-id: OBT:001243
-name: panty liner
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001244
-name: paper gown
-is_a: OBT:000672 ! hospital gown
-
-[Term]
-id: OBT:001245
-name: paper towel
-synonym: "kitchen roll" RELATED [TyDI:52262]
-is_a: OBT:000926 ! towel
-
-[Term]
-id: OBT:001246
-name: parenchyma
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001247
-name: pea family
-synonym: "Fabaceace" EXACT [TyDI:50092]
-synonym: "legume" RELATED [TyDI:50093]
-synonym: "Leguminosae" RELATED [TyDI:50090]
-synonym: "leguminous plant" RELATED [TyDI:50091]
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001248
-name: peptic ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001249
-name: perineal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001250
-name: periodontal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001251
-name: peripheral nervous system
-synonym: "PNS" EXACT [TyDI:53169]
-is_a: OBT:000766 ! nervous system
-
-[Term]
-id: OBT:001252
-name: perirectal area
-synonym: "perianal area" EXACT [TyDI:56377]
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001253
-name: peritoneum
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001254
-name: pet
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:001255
-name: pink pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001256
-name: piping system
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001257
-name: plankton
-synonym: "planktonic" EXACT [TyDI:49767]
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:001258
-name: plant material
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001259
-name: plantlet
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001260
-name: pond
-synonym: "freshwater pond" RELATED [TyDI:51936]
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:001261
-name: pond water
-synonym: "pond" RELATED [TyDI:51935]
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001262
-name: posterior intestinal content
-is_a: OBT:000691 ! intestinal content
-
-[Term]
-id: OBT:001263
-name: potato silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001264
-name: power plant
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001265
-name: prepared meat
-synonym: "processed meat" EXACT [TyDI:51401]
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001266
-name: preserved food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001267
-name: pressed food
-is_a: OBT:000828 ! processed commodity and food
-
-[Term]
-id: OBT:001268
-name: primate part
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001269
-name: probiotic food
-is_a: OBT:000633 ! food for particular diet
-
-[Term]
-id: OBT:001270
-name: public house
-synonym: "tavern" RELATED [TyDI:58118]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001271
-name: public toilet seat
-is_a: OBT:000922 ! toilet seat
-
-[Term]
-id: OBT:001272
-name: purple pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001273
-name: quarry
-is_a: OBT:000624 ! extractive industrial site
-
-[Term]
-id: OBT:001274
-name: rainwater tank
-synonym: "water butt" RELATED [TyDI:58044]
-is_a: OBT:000959 ! water storage system
-
-[Term]
-id: OBT:001275
-name: raw meat
-synonym: "undercooked meat" RELATED [TyDI:51753]
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001276
-name: raw milk
-synonym: "unpasteurized milk" EXACT [TyDI:49881]
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001277
-name: raw seafood
-is_a: OBT:000834 ! raw primary commodities
-
-[Term]
-id: OBT:001278
-name: ready-to-eat meal
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001279
-name: rectal thermometer
-is_a: OBT:000916 ! thermometer as medical device
-
-[Term]
-id: OBT:001280
-name: red pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001281
-name: refinery
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001282
-name: reptile
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:001283
-name: restaurant
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001284
-name: rice silage
-is_a: OBT:000871 ! silage
-
-[Term]
-id: OBT:001285
-name: river
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001286
-name: root cap
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:001287
-name: root cortex part
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:001288
-name: ropy colony
-is_a: OBT:000880 ! smooth colony
-
-[Term]
-id: OBT:001289
-name: ruminant digestive system part
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001290
-name: saline wetland
-synonym: "saline-wetland" EXACT [TyDI:52885]
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001291
-name: saliva
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001292
-name: salt-tolerant plant
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001293
-name: sand
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001294
-name: sandy beach
-is_a: OBT:000855 ! sandy soil
-
-[Term]
-id: OBT:001295
-name: sandy bulk soil
-is_a: OBT:000533 ! bulk soil
-
-[Term]
-id: OBT:001296
-name: sanitary towel
-synonym: "menstrual pad" RELATED [TyDI:56761]
-synonym: "sanitary napkin" RELATED [TyDI:56762]
-synonym: "sanitary pad" RELATED [TyDI:56763]
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001297
-name: sap
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001298
-name: sawmill
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001299
-name: sclerenchyma
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001300
-name: sea ice
-is_a: OBT:000681 ! ice
-
-[Term]
-id: OBT:001301
-name: seafood and seafood product
-synonym: "fresh water food" RELATED [TyDI:51756]
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001302
-name: sebum
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001303
-name: sediment
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001304
-name: seedling
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001305
-name: self-heated organic material
-is_a: OBT:000585 ! dead matter
-
-[Term]
-id: OBT:001306
-name: semen
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001307
-name: sewage
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001308
-name: sewage oxidation pond
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001309
-name: sewage sludge
-is_a: OBT:000611 ! effluent
-
-[Term]
-id: OBT:001310
-name: shale sandstone
-is_a: OBT:000853 ! sandstone
-
-[Term]
-id: OBT:001311
-name: shampoo
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001312
-name: shaving cream
-synonym: "shaving foam" RELATED [TyDI:56839]
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001313
-name: ship scrapping waste
-is_a: OBT:000685 ! industrial waste
-
-[Term]
-id: OBT:001314
-name: shore
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001315
-name: shoreline
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001316
-name: silcone rubber voice prothesis
-is_a: OBT:000701 ! laryngeal prosthetic device
-
-[Term]
-id: OBT:001317
-name: silt
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:001318
-name: silver pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001319
-name: skeleton
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001320
-name: skin ulcer
-is_a: OBT:000933 ! ulcer
-
-[Term]
-id: OBT:001321
-name: slaughtering product
-is_a: OBT:000489 ! animal product and primary derivative thereof
-
-[Term]
-id: OBT:001322
-name: slaugterhouse equipment
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:001323
-name: snack
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001324
-name: soap
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001325
-name: soft tissue abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001326
-name: solfataric soil
-is_a: OBT:000950 ! volcanic soil
-
-[Term]
-id: OBT:001327
-name: solid agricultural waste
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001328
-name: soup
-is_a: OBT:000711 ! liquid food
-
-[Term]
-id: OBT:001329
-name: spirillum
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001330
-name: spirochete
-is_a: OBT:000888 ! spiral-shaped
-
-[Term]
-id: OBT:001331
-name: splenic abcess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001332
-name: sponge
-is_a: OBT:000820 ! porifera
-
-[Term]
-id: OBT:001333
-name: spring
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001334
-name: sprout
-is_a: OBT:000655 ! growing plant
-
-[Term]
-id: OBT:001335
-name: sputum
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001336
-name: stem part
-is_a: OBT:000545 ! caulosphere part
-
-[Term]
-id: OBT:001337
-name: stew
-is_a: OBT:000570 ! composite food
-
-[Term]
-id: OBT:001338
-name: stratified water
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001339
-name: subcutaneous abscess-like lesion
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001340
-name: sugar
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:001341
-name: surface of cheese
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001342
-name: surface smear
-is_a: OBT:000902 ! surface of food
-
-[Term]
-id: OBT:001343
-name: surgical gown
-is_a: OBT:000672 ! hospital gown
-
-[Term]
-id: OBT:001344
-name: swamp
-synonym: "swamp forest" EXACT [TyDI:49819]
-synonym: "wooded swamp" EXACT [TyDI:49818]
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001345
-name: sweat
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001346
-name: tail
-is_a: OBT:000751 ! musculoskeletal system part
-
-[Term]
-id: OBT:001347
-name: take-away restaurant
-synonym: "take away restaurant" RELATED [TyDI:58194]
-synonym: "takeaway shop" RELATED [TyDI:58195]
-synonym: "takeout restaurant" RELATED [TyDI:58196]
-is_a: OBT:000607 ! eating and drinking place
-
-[Term]
-id: OBT:001348
-name: tampon
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001349
-name: tank water
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001350
-name: tears
-synonym: "tear" EXACT [TyDI:49813]
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001351
-name: teat
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001352
-name: teat canal
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001353
-name: temperature sensor
-synonym: "temperature probe" RELATED [TyDI:51770]
-is_a: OBT:000864 ! sensor
-
-[Term]
-id: OBT:001354
-name: terrestial wetland
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:001355
-name: tidal creek
-is_a: OBT:000690 ! intertidal zone
-
-[Term]
-id: OBT:001356
-name: toothbrush
-is_a: OBT:000923 ! toiletries
-
-[Term]
-id: OBT:001357
-name: toothpaste
-synonym: "dentifrice" RELATED [TyDI:56853]
-is_a: OBT:000574 ! cosmetics
-
-[Term]
-id: OBT:001358
-name: trachea
-is_a: OBT:000529 ! broncho-pulmonary segment
-
-[Term]
-id: OBT:001359
-name: treated wood
-is_a: OBT:000586 ! dead wood
-is_a: OBT:003742 ! wood waste
-
-[Term]
-id: OBT:001360
-name: tree
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001361
-name: trunk
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001362
-name: tuber
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:001363
-name: twig
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001364
-name: udder parenchyma
-is_a: OBT:000723 ! mammalian part
-
-[Term]
-id: OBT:001365
-name: university
-is_a: OBT:000838 ! research and study center
-
-[Term]
-id: OBT:001366
-name: upper gastrointestinal tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:001367
-name: urine
-is_a: OBT:000622 ! excreta
-
-[Term]
-id: OBT:001368
-name: vaginal abscess
-is_a: OBT:000476 ! abscess
-
-[Term]
-id: OBT:001369
-name: vaginal secretion
-is_a: OBT:000863 ! secretion
-
-[Term]
-id: OBT:001370
-name: vascular tissue
-is_a: OBT:000816 ! plant tissue
-
-[Term]
-id: OBT:001371
-name: vegetable garden soil
-is_a: OBT:000639 ! garden soil
-
-[Term]
-id: OBT:001372
-name: violet pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001373
-name: warehouse
-synonym: "storehouse" RELATED [TyDI:51804]
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:001374
-name: warm-blooded animal
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:001375
-name: waste food compost
-is_a: OBT:000571 ! compost
-
-[Term]
-id: OBT:001376
-name: water canal
-synonym: "canal" EXACT [TyDI:51944]
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:001377
-name: water column
-is_a: OBT:000704 ! lentic water
-
-[Term]
-id: OBT:001378
-name: water heater
-synonym: "hot water system " RELATED [TyDI:57043]
-synonym: "storage water heater" RELATED [TyDI:57044]
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:001379
-name: water of an humidifier
-is_a: OBT:000957 ! water from air and water system
-
-[Term]
-id: OBT:001380
-name: water system
-synonym: "water supply" RELATED [TyDI:51773]
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:001381
-name: water tank
-synonym: "water storage tank" EXACT [TyDI:53205]
-is_a: OBT:000597 ! drinking water facility
-
-[Term]
-id: OBT:001382
-name: white pigmented
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001383
-name: wood
-is_a: OBT:000927 ! tree part
-
-[Term]
-id: OBT:001384
-name: working animal
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:001385
-name: worm
-is_a: OBT:000694 ! invertebrate species
-
-[Term]
-id: OBT:001386
-name: yellow pigmented
-synonym: "yellowish" RELATED [TyDI:57376]
-is_a: OBT:000809 ! pigmented
-
-[Term]
-id: OBT:001387
-name: yolk sac
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:001388
-name: Achillea millefolium
-is_a: OBT:000972 ! Asteraceae
-
-[Term]
-id: OBT:001389
-name: Allium
-is_a: OBT:001021 ! bulbous plant
-
-[Term]
-id: OBT:001390
-name: Arabidopsis
-is_a: OBT:001213 ! model plant
-
-[Term]
-id: OBT:001391
-name: Brassica
-is_a: OBT:001057 ! crucifer
-
-[Term]
-id: OBT:001392
-name: Osmitopsis asteriscoides
-is_a: OBT:000972 ! Asteraceae
-
-[Term]
-id: OBT:001393
-name: Salicornioideae
-is_a: OBT:001292 ! salt-tolerant plant
-
-[Term]
-id: OBT:001394
-name: abomasum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001395
-name: adult animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001396
-name: aioli
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001397
-name: alcoholic drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001398
-name: algae and related product
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001399
-name: alkaline lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001400
-name: alligator
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001401
-name: almond and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001402
-name: almond tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001403
-name: amaranth and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001404
-name: amphibian and product thereof
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001405
-name: anaerobic mud
-synonym: "anoxic mud" EXACT [TyDI:53789]
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001406
-name: anaerobic sediment
-synonym: "anoxic sediment" EXACT [TyDI:53756]
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001407
-name: animal blood and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001408
-name: animal bone and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001409
-name: animal bone marrow and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001410
-name: animal brain and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001411
-name: animal foot and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001412
-name: animal head and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001413
-name: animal heart and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001414
-name: animal kidney and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001415
-name: animal liver and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001416
-name: animal manure
-is_a: OBT:000985 ! animal waste
-
-[Term]
-id: OBT:001417
-name: animal marrowbone
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001418
-name: animal neck and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001419
-name: animal roe and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001420
-name: animal skin and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001421
-name: animal stomach and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001422
-name: animal tail and product thereof
-is_a: OBT:001321 ! slaughtering product
-
-[Term]
-id: OBT:001423
-name: animal tongue and product thereof
-is_a: OBT:001234 ! offal and product thereof
-
-[Term]
-id: OBT:001424
-name: ant
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001425
-name: anther
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001426
-name: anther part
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001427
-name: aorta
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001428
-name: aphid
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001429
-name: appendix
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001430
-name: aquatic sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001431
-name: aquifer sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001432
-name: arm
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001433
-name: aromatic product and primary derivative thereof
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001434
-name: arsenate treated wood
-is_a: OBT:001359 ! treated wood
-
-[Term]
-id: OBT:001435
-name: avian crop
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001436
-name: bakery product
-synonym: "baked good" RELATED [TyDI:50595]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001437
-name: basophil
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:001438
-name: beach mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001439
-name: bean and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001440
-name: bechamel sauce
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001441
-name: bee
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001442
-name: berry and small fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001443
-name: bio clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001444
-name: biofilm forming
-is_a: OBT:001005 ! biofilm phenotype
-
-[Term]
-id: OBT:001445
-name: birch
-synonym: "birch tree" EXACT []
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001446
-name: bird
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:001447
-name: bird meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001448
-name: birria
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:001449
-name: black anoxic freshwater mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001450
-name: black sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001451
-name: blade
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001452
-name: blanket bog peat
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001453
-name: blood-feeding insect
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001454
-name: borax leachate
-is_a: OBT:001173 ! leachate
-
-[Term]
-id: OBT:001455
-name: borehole
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001456
-name: bottle
-is_a: OBT:001110 ! food container
-
-[Term]
-id: OBT:001457
-name: brackish pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001458
-name: bran
-is_a: OBT:001209 ! milled food
-
-[Term]
-id: OBT:001459
-name: brassica vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001460
-name: breakfast cereal
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001461
-name: brisket saw
-synonym: "mechanical saw" RELATED [TyDI:57225]
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001462
-name: buckwheat and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001463
-name: bud
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:001464
-name: bug
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001465
-name: bulb vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001466
-name: burger
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001467
-name: butcher's knife
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001468
-name: butter
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001469
-name: buttermilk
-synonym: "butter milk" EXACT [TyDI:57950]
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001470
-name: caecal content
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001471
-name: caecum
-synonym: "cecum" EXACT [TyDI:49664]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001472
-name: can
-synonym: "tin" EXACT []
-is_a: OBT:001110 ! food container
-
-[Term]
-id: OBT:001473
-name: canned food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001474
-name: carr
-is_a: OBT:001344 ! swamp
-
-[Term]
-id: OBT:001475
-name: cashew and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001476
-name: cattle dipping
-synonym: "cattle dip" EXACT [TyDI:50013]
-is_a: OBT:001181 ! liquid agricultural waste
-
-[Term]
-id: OBT:001477
-name: cattle-farm compost
-is_a: OBT:001194 ! manure compost
-
-[Term]
-id: OBT:001478
-name: cereal bar
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001479
-name: cereal grain and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001480
-name: cheese
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001481
-name: cheese rind
-is_a: OBT:001114 ! food rind
-
-[Term]
-id: OBT:001482
-name: cheese smear
-is_a: OBT:001342 ! surface smear
-
-[Term]
-id: OBT:001483
-name: chemical weapons factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001484
-name: chia seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001485
-name: chicken coop
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001486
-name: chopstick
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001487
-name: citrus fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001488
-name: cloaca
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001489
-name: coal mine waste
-synonym: "coal refuse" RELATED [TyDI:53145]
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001490
-name: coal-cleaning residue
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001491
-name: coastal lagoon mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001492
-name: coastal sand
-is_a: OBT:001293 ! sand
-
-[Term]
-id: OBT:001493
-name: cockroach
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001494
-name: cocoa bean and primary derivative thereof
-is_a: OBT:001238 ! oilfruit and primary derivative thereof
-
-[Term]
-id: OBT:001495
-name: coconut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001496
-name: colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001497
-name: concentrated food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001498
-name: conifer
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001499
-name: cooked food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001500
-name: cooled food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001501
-name: corn chip
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001502
-name: corn silage
-is_a: OBT:001136 ! grass silage
-
-[Term]
-id: OBT:001503
-name: corn tortillas
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001504
-name: coronary artery
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001505
-name: cream
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001506
-name: cresote treated wood
-is_a: OBT:001359 ! treated wood
-
-[Term]
-id: OBT:001507
-name: crocodile
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001508
-name: crustacean and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001509
-name: cutlery
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001510
-name: cutting table
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001511
-name: dairy parlour waste
-is_a: OBT:001062 ! dairy farming waste
-
-[Term]
-id: OBT:001512
-name: dairy soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001513
-name: dambo
-is_a: OBT:001121 ! freshwater wetland
-
-[Term]
-id: OBT:001514
-name: dark chocolate
-is_a: OBT:001036 ! chocolate product
-
-[Term]
-id: OBT:001515
-name: dashi
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001516
-name: dead animal
-is_a: OBT:001063 ! dead organism
-
-[Term]
-id: OBT:001517
-name: decaying insect-invaded wood
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001518
-name: decaying marine algae
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001519
-name: deep sea mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001520
-name: dental plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001521
-name: dental root
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001522
-name: dental root canal
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001523
-name: digester sludge
-is_a: OBT:001309 ! sewage sludge
-
-[Term]
-id: OBT:001524
-name: ditch mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001525
-name: domestic sewage
-is_a: OBT:001307 ! sewage
-
-[Term]
-id: OBT:001526
-name: dried food
-synonym: "dehydrated food" RELATED [TyDI:51927]
-synonym: "dry foods" EXACT [TyDI:58297]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001527
-name: dried nut
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001528
-name: drilling mud
-is_a: OBT:001211 ! mine drainage
-
-[Term]
-id: OBT:001529
-name: drilling pipe
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001530
-name: drinking water
-synonym: "potable water" RELATED [TyDI:49686]
-synonym: "water" RELATED [TyDI:49685]
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001531
-name: drosophila
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001532
-name: dry forest humus
-is_a: OBT:001120 ! forest humus
-
-[Term]
-id: OBT:001533
-name: duodenal ulcer
-is_a: OBT:001248 ! peptic ulcer
-
-[Term]
-id: OBT:001534
-name: duodenum
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001535
-name: echinoderm and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001536
-name: egg based dish
-synonym: "egg dish" RELATED [TyDI:49858]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001537
-name: egg white
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001538
-name: egg yolk
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001539
-name: elbow
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001540
-name: electronics device industry
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001541
-name: elkhorn coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001542
-name: elm
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001543
-name: embryo
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001544
-name: eosinophil
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:001546
-name: fermented food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001547
-name: fillet
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001548
-name: fish based dish
-synonym: "fish dish" RELATED [TyDI:49864]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001549
-name: fish meat and fish meat product
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001550
-name: fish soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001551
-name: flaxseed and primary derivative thereof
-synonym: "flax seed" RELATED [TyDI:51195]
-synonym: "linseed" EXACT [TyDI:51196]
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001552
-name: flour
-is_a: OBT:001209 ! milled food
-
-[Term]
-id: OBT:001553
-name: fly
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001554
-name: food blender
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001555
-name: food dicing machine
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001556
-name: food fermentation equipment
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001557
-name: food processing factory
-synonym: "food factory" EXACT [TyDI:49609]
-synonym: "food processing plant" EXACT [TyDI:49608]
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001558
-name: food processing waste
-synonym: "food residue" RELATED []
-is_a: OBT:001157 ! industrial organic waste
-
-[Term]
-id: OBT:001559
-name: food slicing machine
-is_a: OBT:001112 ! food processing appliance
-
-[Term]
-id: OBT:001560
-name: fore-stomach
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001561
-name: forest tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001562
-name: fossil stromatolite
-is_a: OBT:001024 ! calcereous rock
-
-[Term]
-id: OBT:001563
-name: freshwater mud
-synonym: "fresh water mud" EXACT [TyDI:55552]
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001564
-name: frozen food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001565
-name: fruit based dish
-synonym: "fruit dish" RELATED [TyDI:57284]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001566
-name: fruit rind
-is_a: OBT:001114 ! food rind
-
-[Term]
-id: OBT:001567
-name: fruit tree
-comment: horticole meaning
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:001568
-name: fruit with edible peel and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001569
-name: fruit with inedible peel and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001570
-name: fruiting vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001571
-name: fuel ethanol production facility
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001572
-name: fuel oil piping system
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:001573
-name: fungi and related product
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001574
-name: funicle
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001575
-name: gas piping system
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:001576
-name: gas tank
-synonym: "gas reservoir" EXACT [TyDI:56799]
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001577
-name: gastric mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001578
-name: gazpacho
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001579
-name: geothermal lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001580
-name: geyser
-is_a: OBT:001333 ! spring
-
-[Term]
-id: OBT:001581
-name: gingival sulcus
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001582
-name: gizzard
-is_a: OBT:001006 ! bird and reptile GIT part
-
-[Term]
-id: OBT:001583
-name: glassy rind of lava
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001584
-name: gold mine
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:001585
-name: green tea leaf
-is_a: OBT:001162 ! ingredient for hot drink
-
-[Term]
-id: OBT:001586
-name: grocery
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001587
-name: guano
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001588
-name: hamburger meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001589
-name: hand
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001590
-name: hazelnut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001591
-name: heartwood
-is_a: OBT:001383 ! wood
-
-[Term]
-id: OBT:001592
-name: heat-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001593
-name: hemp seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001594
-name: high temperature oil field
-is_a: OBT:001235 ! oil field
-
-[Term]
-id: OBT:001595
-name: holoplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001596
-name: honey
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:001597
-name: hot dog
-synonym: "hot-dog" EXACT [TyDI:52584]
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001598
-name: hot drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001599
-name: hot mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001600
-name: hydathode
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001601
-name: ileum
-synonym: "ileum of the small intestine" RELATED [TyDI:49566]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001602
-name: intra-uterine progeny
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001603
-name: ionised food
-synonym: "ionized food" EXACT [TyDI:53475]
-synonym: "irradiated food" RELATED [TyDI:53474]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001604
-name: jarred food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001605
-name: jejunum
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001606
-name: jellyfish and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001607
-name: jointvetch
-synonym: "Aeschynomene" EXACT [TyDI:52426]
-is_a: OBT:001247 ! pea family
-
-[Term]
-id: OBT:001608
-name: knee
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001609
-name: larvae
-synonym: "larval" RELATED [TyDI:51296]
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001610
-name: latex processing factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001611
-name: leaf margin
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001612
-name: leafhopper
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001613
-name: leafy vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001614
-name: leech
-is_a: OBT:000987 ! annelid
-
-[Term]
-id: OBT:001615
-name: legume based dish
-synonym: "legume dish" RELATED [TyDI:49764]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001616
-name: legume soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001617
-name: lentil and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001618
-name: lime soap
-is_a: OBT:001324 ! soap
-
-[Term]
-id: OBT:001619
-name: liquid egg product
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001620
-name: litter
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001621
-name: livestock barn
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001622
-name: lupin and related product
-synonym: "lupine" EXACT [TyDI:51239]
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001623
-name: lymphocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:001624
-name: mammal meat
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001625
-name: mammalian
-synonym: "mammal" RELATED [TyDI:49573]
-synonym: "mammalia" RELATED [TyDI:49572]
-synonym: "mammalia-associated habitat" EXACT [TyDI:49571]
-synonym: "mammalian host" RELATED [TyDI:49574]
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:001626
-name: manufacture
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001627
-name: manure
-is_a: OBT:001181 ! liquid agricultural waste
-
-[Term]
-id: OBT:001628
-name: maple tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001629
-name: marinated food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001630
-name: marine crustacean
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:001631
-name: marine mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001632
-name: market garden plant
-is_a: OBT:001125 ! garden plant
-
-[Term]
-id: OBT:001633
-name: mayonnaise
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001634
-name: meat based dish
-synonym: "meat dish" RELATED [TyDI:49695]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001635
-name: meat hook
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:001636
-name: meat juice
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001637
-name: meat soup
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001638
-name: meatball
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001639
-name: meringue
-is_a: OBT:001045 ! confectionery
-
-[Term]
-id: OBT:001640
-name: meromictic lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001641
-name: meroplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001642
-name: mesenteric artery
-is_a: OBT:000990 ! artery
-
-[Term]
-id: OBT:001643
-name: methane seep
-is_a: OBT:001127 ! gas seep
-
-[Term]
-id: OBT:001644
-name: midrib
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001645
-name: milk
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001646
-name: milk chocolate
-is_a: OBT:001036 ! chocolate product
-
-[Term]
-id: OBT:001647
-name: mining slag heap
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001648
-name: mite
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001649
-name: mixed cereal-based snack
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001650
-name: mixed dish
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001651
-name: mollusc and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001652
-name: moth
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001653
-name: mouth
-synonym: "oral" RELATED [TyDI:49560]
-synonym: "oral cavity" RELATED [TyDI:49561]
-is_a: OBT:001020 ! buccal
-
-[Term]
-id: OBT:001654
-name: mucosal surface
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001655
-name: mud sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001656
-name: mudflat
-is_a: OBT:001041 ! coastal wetland
-
-[Term]
-id: OBT:001657
-name: muesli
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001658
-name: mummy tissue
-is_a: OBT:001064 ! dead tissue
-
-[Term]
-id: OBT:001659
-name: mushroom based dish
-synonym: "mushroom dish" RELATED [TyDI:49770]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001660
-name: mustard
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001661
-name: nasopharyngeal mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001662
-name: newborn animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001663
-name: nitrogen fertilizer factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001664
-name: non-biofilm forming
-is_a: OBT:001005 ! biofilm phenotype
-
-[Term]
-id: OBT:001665
-name: nut
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001666
-name: oak
-synonym: "oak tree" EXACT []
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001667
-name: obligate methanotroph
-is_a: OBT:001205 ! methanotroph
-
-[Term]
-id: OBT:001668
-name: oesophagus
-synonym: "gullet" EXACT [TyDI:49622]
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001669
-name: offshore oil industry
-is_a: OBT:001236 ! oil industry
-
-[Term]
-id: OBT:001670
-name: offspring
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001671
-name: oil pipeline
-synonym: "petroleum pipeline" RELATED [TyDI:52513]
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001672
-name: oil reservoir
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001673
-name: oil seep
-synonym: "petroleum seep" EXACT [TyDI:53778]
-is_a: OBT:001058 ! crude oil
-
-[Term]
-id: OBT:001674
-name: oil spill
-is_a: OBT:001212 ! mine waste
-
-[Term]
-id: OBT:001675
-name: oil-water separator
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001676
-name: okpehe
-is_a: OBT:001328 ! soup
-
-[Term]
-id: OBT:001677
-name: omasum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001678
-name: open pit mine
-synonym: "opencast mine" EXACT [TyDI:52676]
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:001679
-name: orange storehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001680
-name: organic leachate
-is_a: OBT:001173 ! leachate
-
-[Term]
-id: OBT:001681
-name: ornemental tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001682
-name: ovary wall
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001683
-name: ovule
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001684
-name: ovule part
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001685
-name: packaging clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001686
-name: packaging factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001687
-name: packed food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001688
-name: paisa mire
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001689
-name: palagonite rind
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001690
-name: palisade layer
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001691
-name: paper mill
-synonym: "paper factory" EXACT [TyDI:52691]
-synonym: "pulp and paper mill" RELATED [TyDI:52690]
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001692
-name: paper mill sludge
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001693
-name: parasitic nematode
-is_a: OBT:001230 ! nematode
-
-[Term]
-id: OBT:001694
-name: pasta and related product
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001695
-name: pasta based dish
-synonym: "pasta dish" RELATED [TyDI:49790]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001696
-name: pea and related product
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001697
-name: peanut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001698
-name: peat cut
-synonym: "peat cutting" EXACT [TyDI:53772]
-is_a: OBT:001258 ! plant material
-
-[Term]
-id: OBT:001699
-name: peat swamp forest
-synonym: "peat swamp" EXACT [TyDI:53765]
-is_a: OBT:001344 ! swamp
-
-[Term]
-id: OBT:001700
-name: peatland
-synonym: "peat bog" RELATED [TyDI:51535]
-synonym: "peat cutting area" RELATED [TyDI:51533]
-synonym: "peatbog" RELATED [TyDI:51534]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001701
-name: pecan and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001702
-name: pericarp
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001703
-name: periodontal pocket
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001704
-name: periodontium
-synonym: "periodontal" RELATED [TyDI:52665]
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001705
-name: permafrost sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001706
-name: pesto
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001707
-name: petal
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001708
-name: petiole
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001709
-name: petrochemical factory
-is_a: OBT:001031 ! chemical plant
-
-[Term]
-id: OBT:001710
-name: petroleum refinery
-is_a: OBT:001281 ! refinery
-
-[Term]
-id: OBT:001711
-name: petroleum reservoir
-is_a: OBT:001094 ! extractive industry equipment
-
-[Term]
-id: OBT:001712
-name: phenotype wrt chemical composition
-is_a: OBT:000023 ! phenotype wrt stress
-is_a: OBT:000127 ! phenotype wrt habitat acidity
-
-[Term]
-id: OBT:001713
-name: phloem
-is_a: OBT:001370 ! vascular tissue
-
-[Term]
-id: OBT:001714
-name: phytoplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001715
-name: pine forest
-is_a: OBT:003881 ! conifer forest
-
-[Term]
-id: OBT:001716
-name: pine forest humus
-is_a: OBT:001120 ! forest humus
-
-[Term]
-id: OBT:001717
-name: pistachio and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001718
-name: agricultural plant residue
-synonym: "agricultural plant waste" NARROW []
-is_a: OBT:000478 ! agricultural waste
-
-[Term]
-id: OBT:001719
-name: pocosin
-is_a: OBT:001121 ! freshwater wetland
-
-[Term]
-id: OBT:001720
-name: polar sea ice
-is_a: OBT:001300 ! sea ice
-
-[Term]
-id: OBT:001721
-name: pollen tube
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001722
-name: pome fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001723
-name: poppy seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001724
-name: potato plant
-is_a: OBT:001362 ! tuber
-
-[Term]
-id: OBT:001725
-name: potato based dish
-synonym: "potato dish" RELATED [TyDI:49705]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001726
-name: potato chip
-synonym: "potato crisp" RELATED [TyDI:51417]
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001727
-name: poultry house
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001728
-name: powdered food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001729
-name: pressure treated food
-synonym: "pressure processed food" RELATED [TyDI:53464]
-synonym: "pressure-treated food" RELATED [TyDI:53467]
-synonym: "pressuretreated food" EXACT [TyDI:53465]
-synonym: "pressurized food" RELATED [TyDI:53466]
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001730
-name: progeny
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001731
-name: pumpkin seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001732
-name: pupa
-synonym: "pupal" RELATED [TyDI:51317]
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001733
-name: quiche
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001734
-name: quinoa and primary derivative thereof
-synonym: "quinoa seed" EXACT [TyDI:51226]
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001735
-name: raised mire
-synonym: "raised bog" RELATED [TyDI:51528]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001736
-name: raw dough
-synonym: "dough" EXACT [TyDI:50582]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-
-[Term]
-id: OBT:001737
-name: rectal swab
-is_a: OBT:001102 ! feces
-
-[Term]
-id: OBT:001738
-name: rectum
-synonym: "rectal" RELATED [TyDI:55347]
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001739
-name: red clay
-is_a: OBT:001037 ! clay
-
-[Term]
-id: OBT:001740
-name: red-pigmented bacteriome
-is_a: OBT:000998 ! bacteriome
-
-[Term]
-id: OBT:001741
-name: reef
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001742
-name: reptile and product thereof
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001743
-name: reticulum
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001744
-name: rice based dish
-synonym: "rice dish" RELATED [TyDI:49793]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001745
-name: rice chip
-is_a: OBT:001323 ! snack
-
-[Term]
-id: OBT:001746
-name: roasted coffee bean
-is_a: OBT:001162 ! ingredient for hot drink
-
-[Term]
-id: OBT:001747
-name: root and tuber vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001748
-name: rotting hay
-is_a: OBT:001065 ! decaying matter
-
-[Term]
-id: OBT:001749
-name: rumen
-is_a: OBT:001289 ! ruminant digestive system part
-
-[Term]
-id: OBT:001750
-name: rye grass silage
-is_a: OBT:001136 ! grass silage
-
-[Term]
-id: OBT:001751
-name: saline sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001752
-name: salivary gland
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001753
-name: salt
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001754
-name: salt lake mud
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001755
-name: salt-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001756
-name: sandwich
-is_a: OBT:001278 ! ready-to-eat meal
-
-[Term]
-id: OBT:001757
-name: sandy sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001758
-name: sausage
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001759
-name: saw mill
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001760
-name: scleractinian coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001761
-name: sea sand
-is_a: OBT:001293 ! sand
-
-[Term]
-id: OBT:001762
-name: seafood based dish
-synonym: "seafood dish" RELATED [TyDI:49781]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001763
-name: seagrass
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001764
-name: sedimentation pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001765
-name: seed
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001766
-name: seed part
-is_a: OBT:001123 ! fruit part
-
-[Term]
-id: OBT:001767
-name: sepal
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001768
-name: sesame seed and primary derivative thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001769
-name: shallow pond
-is_a: OBT:001260 ! pond
-
-[Term]
-id: OBT:001770
-name: shoe factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001771
-name: shrub
-is_a: OBT:001125 ! garden plant
-
-[Term]
-id: OBT:001772
-name: sigmoid colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001773
-name: sludge
-is_a: OBT:001221 ! mud
-
-[Term]
-id: OBT:001774
-name: smoked food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001775
-name: smooth cord grass
-synonym: "Spartina alterniflora" EXACT [TyDI:50533]
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001776
-name: snail
-is_a: OBT:001215 ! mollusc
-
-[Term]
-id: OBT:001777
-name: snake
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001778
-name: soda
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001779
-name: soft drink
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001780
-name: solar lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001781
-name: soybean and related product
-synonym: "soy and related product" RELATED [TyDI:51059]
-synonym: "soyabean and related product" RELATED [TyDI:51060]
-is_a: OBT:001177 ! legume seed and primary derivative thereof
-
-[Term]
-id: OBT:001782
-name: spacecraft assembly clean room
-is_a: OBT:001038 ! clean room
-
-[Term]
-id: OBT:001783
-name: sphagnum bog
-synonym: "acidic Sphagnum peat bog" RELATED [TyDI:52686]
-synonym: "Sphagnum peat bog" RELATED [TyDI:52687]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001784
-name: spice
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001785
-name: spider
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001786
-name: stall
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001787
-name: star coral
-is_a: OBT:001048 ! coral
-
-[Term]
-id: OBT:001788
-name: stem cortex part
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:001789
-name: stem vegetable
-is_a: OBT:001126 ! garden vegetable and primary derivative thereof
-
-[Term]
-id: OBT:001790
-name: stigma
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001791
-name: stink bug
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001792
-name: stomach
-is_a: OBT:001366 ! upper gastrointestinal tract part
-
-[Term]
-id: OBT:001793
-name: stomach mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001794
-name: stomach ulcer
-is_a: OBT:001248 ! peptic ulcer
-
-[Term]
-id: OBT:001795
-name: stomata
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001796
-name: stone fruit and primary derivative thereof
-is_a: OBT:001122 ! fruit and primary derivative thereof
-
-[Term]
-id: OBT:001797
-name: stratified lake
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:001798
-name: style
-is_a: OBT:001106 ! flower part
-
-[Term]
-id: OBT:001799
-name: subgingiva
-synonym: "subgingival" RELATED [TyDI:57906]
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001800
-name: subgingival plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001801
-name: submarine basalt
-is_a: OBT:001196 ! marine rock
-
-[Term]
-id: OBT:001802
-name: sugar confectionery
-synonym: "candy" RELATED [TyDI:57248]
-is_a: OBT:001045 ! confectionery
-
-[Term]
-id: OBT:001803
-name: sugar-beet plant
-synonym: "betroot plant" EXACT [TyDI:49625]
-is_a: OBT:001362 ! tuber
-
-[Term]
-id: OBT:001804
-name: sugar-preserved food
-is_a: OBT:001266 ! preserved food
-
-[Term]
-id: OBT:001805
-name: sunflower seed and primary derivatives thereof
-is_a: OBT:001132 ! grain and primary derivative thereof
-
-[Term]
-id: OBT:001806
-name: supragingival plaque
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001807
-name: surface sediment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:001808
-name: sweet clover
-synonym: "Melilotus albus" EXACT [TyDI:52622]
-is_a: OBT:001247 ! pea family
-
-[Term]
-id: OBT:001809
-name: swine house
-synonym: "swine barn" RELATED [TyDI:57772]
-is_a: OBT:001183 ! livestock habitat
-
-[Term]
-id: OBT:001810
-name: tannery
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001811
-name: tannery sludge
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001812
-name: tea tree
-is_a: OBT:001360 ! tree
-
-[Term]
-id: OBT:001813
-name: terminal ileum
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001814
-name: termite
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001815
-name: terrestrial crustacean
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:001816
-name: terrestrial invertebrate product
-is_a: OBT:001200 ! meat and meat product
-
-[Term]
-id: OBT:001817
-name: textile dye effluent
-is_a: OBT:001159 ! industrial sludge
-
-[Term]
-id: OBT:001818
-name: textile mill
-synonym: "textile factory" NARROW []
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001819
-name: thermal power plant
-is_a: OBT:001264 ! power plant
-
-[Term]
-id: OBT:001820
-name: thermal spring
-is_a: OBT:001333 ! spring
-
-[Term]
-id: OBT:001821
-name: tick
-is_a: OBT:000989 ! arachnid
-
-[Term]
-id: OBT:001822
-name: tobacco warehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001823
-name: toe
-is_a: OBT:001268 ! primate part
-
-[Term]
-id: OBT:001824
-name: tomato ketchup
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:001825
-name: tongue
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001826
-name: tooth
-synonym: "dental" EXACT [TyDI:52708]
-is_a: OBT:001217 ! mouth part
-
-[Term]
-id: OBT:001827
-name: toothpick
-is_a: OBT:001084 ! eating utensil
-
-[Term]
-id: OBT:001828
-name: tortoise
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001829
-name: transverse colon
-is_a: OBT:001184 ! lower gastrointestinal tract part
-
-[Term]
-id: OBT:001830
-name: tundra mire
-synonym: "subarctic mire" RELATED [TyDI:53775]
-is_a: OBT:001009 ! bog
-
-[Term]
-id: OBT:001831
-name: tunicate and product thereof
-synonym: "sea squirt" RELATED [TyDI:49810]
-is_a: OBT:001301 ! seafood and seafood product
-
-[Term]
-id: OBT:001832
-name: turtle
-is_a: OBT:001282 ! reptile
-
-[Term]
-id: OBT:001833
-name: vaginal swab
-is_a: OBT:001369 ! vaginal secretion
-
-[Term]
-id: OBT:001834
-name: vegetable based dish
-synonym: "vegetable dish" RELATED [TyDI:49776]
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001835
-name: vein
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:001836
-name: vestibular mucosa
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:001837
-name: vitamin supplement
-is_a: OBT:001070 ! dietary supplement
-
-[Term]
-id: OBT:001838
-name: walnut and primary derivative thereof
-is_a: OBT:001232 ! nut and primary derivative thereof
-
-[Term]
-id: OBT:001839
-name: war readiness warehouse
-is_a: OBT:001373 ! warehouse
-
-[Term]
-id: OBT:001840
-name: wasp
-is_a: OBT:001163 ! insect
-
-[Term]
-id: OBT:001841
-name: water based beverage
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:001842
-name: water based dish
-is_a: OBT:001073 ! dish
-
-[Term]
-id: OBT:001843
-name: water dispenser
-is_a: OBT:001082 ! drinking water supply
-
-[Term]
-id: OBT:001844
-name: water in cooling tower
-is_a: OBT:001047 ! cooling water
-
-[Term]
-id: OBT:001845
-name: weed
-is_a: OBT:001135 ! grass plant
-
-[Term]
-id: OBT:001846
-name: whey
-is_a: OBT:001208 ! milk and milk product
-
-[Term]
-id: OBT:001847
-name: whole egg
-is_a: OBT:001086 ! egg and egg product
-
-[Term]
-id: OBT:001848
-name: xylem
-is_a: OBT:001370 ! vascular tissue
-
-[Term]
-id: OBT:001849
-name: young animal
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:001850
-name: zinc factory
-is_a: OBT:001097 ! factory
-
-[Term]
-id: OBT:001851
-name: zooplankton
-is_a: OBT:001257 ! plankton
-
-[Term]
-id: OBT:001852
-name: Aeschynomene indica
-is_a: OBT:001607 ! jointvetch
-
-[Term]
-id: OBT:001853
-name: Arabidopsis thaliana
-is_a: OBT:001390 ! Arabidopsis
-
-[Term]
-id: OBT:001854
-name: Intertidal sand
-is_a: OBT:001492 ! coastal sand
-
-[Term]
-id: OBT:001855
-name: UHT food
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:001856
-name: activated sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001857
-name: agricultural soil
-is_a: OBT:000004 ! animal husbandry and agricultural habitat
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:001858
-name: algae as food
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:001859
-name: almond as food
-is_a: OBT:001401 ! almond and primary derivative thereof
-
-[Term]
-id: OBT:001860
-name: amaranth
-is_a: OBT:001403 ! amaranth and primary derivative thereof
-
-[Term]
-id: OBT:001861
-name: anaerobic digester sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001862
-name: anaerobic sewage sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001863
-name: animal blood
-is_a: OBT:001407 ! animal blood and product thereof
-
-[Term]
-id: OBT:001864
-name: animal bone
-is_a: OBT:001408 ! animal bone and product thereof
-
-[Term]
-id: OBT:001865
-name: animal brain
-is_a: OBT:001410 ! animal brain and product thereof
-
-[Term]
-id: OBT:001866
-name: animal foot
-is_a: OBT:001411 ! animal foot and product thereof
-
-[Term]
-id: OBT:001867
-name: animal head
-is_a: OBT:001412 ! animal head and product thereof
-
-[Term]
-id: OBT:001868
-name: animal heart
-is_a: OBT:001413 ! animal heart and product thereof
-
-[Term]
-id: OBT:001869
-name: animal kidney
-is_a: OBT:001414 ! animal kidney and product thereof
-
-[Term]
-id: OBT:001870
-name: animal liver
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:001871
-name: animal neck
-is_a: OBT:001418 ! animal neck and product thereof
-
-[Term]
-id: OBT:001872
-name: animal roe
-is_a: OBT:001419 ! animal roe and product thereof
-
-[Term]
-id: OBT:001873
-name: animal skin
-is_a: OBT:001420 ! animal skin and product thereof
-
-[Term]
-id: OBT:001874
-name: animal stomach
-is_a: OBT:001421 ! animal stomach and product thereof
-
-[Term]
-id: OBT:001875
-name: animal tail
-is_a: OBT:001422 ! animal tail and product thereof
-
-[Term]
-id: OBT:001876
-name: animal tongue
-is_a: OBT:001423 ! animal tongue and product thereof
-
-[Term]
-id: OBT:001877
-name: anoxic sewage sludge
-is_a: OBT:001523 ! digester sludge
-
-[Term]
-id: OBT:001878
-name: antelope
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001879
-name: apple and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:001880
-name: apple tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001881
-name: apricot and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:001882
-name: armadillo
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001883
-name: artichoke and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001884
-name: arugula
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001885
-name: aspargus and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001886
-name: aubergine and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001887
-name: avocado and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:001888
-name: baby corn and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001889
-name: baked food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001890
-name: bamboo shoot and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001891
-name: banana and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:001892
-name: banana tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001893
-name: barley and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:001894
-name: basil and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001895
-name: bat
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001896
-name: beach sand
-is_a: OBT:001492 ! coastal sand
-
-[Term]
-id: OBT:001897
-name: bean
-is_a: OBT:001439 ! bean and related product
-
-[Term]
-id: OBT:001898
-name: bear
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001899
-name: beef
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:001900
-name: beetroot and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001901
-name: berry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001902
-name: biscuit
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001903
-name: blackberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001904
-name: blackcurrant and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001905
-name: blanched food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001906
-name: blood sausage
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:001907
-name: blueberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001908
-name: boiled food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:001909
-name: bottled water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:001910
-name: bottling factory
-is_a: OBT:001686 ! packaging factory
-
-[Term]
-id: OBT:001911
-name: bouillabaisse
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:001912
-name: bovine milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001913
-name: bread
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001914
-name: bread pre mix
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:001915
-name: broccoli and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001916
-name: brussel sprout and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001917
-name: buckwheat
-is_a: OBT:001462 ! buckwheat and primary derivative thereof
-
-[Term]
-id: OBT:001918
-name: buffalo milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001919
-name: bumblebee
-is_a: OBT:001441 ! bee
-
-[Term]
-id: OBT:001920
-name: bun
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001921
-name: cake pre mix
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:001922
-name: calf barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001923
-name: camel
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:001924
-name: camel milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001925
-name: canal of root filled tooth
-is_a: OBT:001522 ! dental root canal
-
-[Term]
-id: OBT:001926
-name: candied food
-is_a: OBT:001804 ! sugar-preserved food
-
-[Term]
-id: OBT:001927
-name: canned fish
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001928
-name: canned meat
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001929
-name: canned seafood
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001930
-name: canning factory
-is_a: OBT:001686 ! packaging factory
-
-[Term]
-id: OBT:001931
-name: cantaloupe rind
-synonym: "cantaloupe surface" RELATED [TyDI:57986]
-is_a: OBT:001566 ! fruit rind
-
-[Term]
-id: OBT:001932
-name: caramel
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:001933
-name: cardoon and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001934
-name: carrot and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001935
-name: cashew apple
-is_a: OBT:001475 ! cashew and primary derivative thereof
-
-[Term]
-id: OBT:001936
-name: cashew seed
-is_a: OBT:001475 ! cashew and primary derivative thereof
-
-[Term]
-id: OBT:001937
-name: cauliflower and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001938
-name: celeriac and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:001939
-name: celery and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:001940
-name: celery leaf and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001941
-name: cep and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:001942
-name: ceviche
-synonym: "cebiche" EXACT [TyDI:57281]
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:001943
-name: chard and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001944
-name: cheese brine
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:001945
-name: cheeseburger
-is_a: OBT:001466 ! burger
-
-[Term]
-id: OBT:001946
-name: cherry and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:001947
-name: chewing gum
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:001948
-name: chia seed
-is_a: OBT:001484 ! chia seed and primary derivative thereof
-
-[Term]
-id: OBT:001949
-name: chicken house
-is_a: OBT:001727 ! poultry house
-
-[Term]
-id: OBT:001950
-name: chili pepper and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001951
-name: chinese cabbage and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001952
-name: chipolata
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:001953
-name: chive and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:001954
-name: cinnamon and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001955
-name: citronella grass and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001956
-name: citrus tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001957
-name: clove and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:001958
-name: coal spoil heap
-is_a: OBT:001489 ! coal mine waste
-
-[Term]
-id: OBT:001959
-name: cocktail drink
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:001960
-name: cocoa
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001961
-name: cocoa bean
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001962
-name: cocoa beverage
-is_a: OBT:001598 ! hot drink
-
-[Term]
-id: OBT:001963
-name: cocoa butter
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001964
-name: cocoa powder
-is_a: OBT:001494 ! cocoa bean and primary derivative thereof
-
-[Term]
-id: OBT:001965
-name: coconut as food
-is_a: OBT:001495 ! coconut and primary derivative thereof
-
-[Term]
-id: OBT:001966
-name: coffee beverage
-is_a: OBT:001598 ! hot drink
-
-[Term]
-id: OBT:001967
-name: collard green
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:001968
-name: common mushroom and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:001969
-name: compote
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:001970
-name: contaminated drinking water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:001971
-name: cooked fish
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:001972
-name: courgette and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001973
-name: couscous
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:001974
-name: cow barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001975
-name: cow milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:001976
-name: crab
-is_a: OBT:001630 ! marine crustacean
-
-[Term]
-id: OBT:001977
-name: crab and product thereof
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:001978
-name: cracker
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:001979
-name: cranberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:001980
-name: crocodile product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:001981
-name: cucumber and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:001982
-name: cultivated field
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:000092 ! field
-
-[Term]
-id: OBT:001983
-name: cumin
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:001984
-name: cured food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:001985
-name: curry powder
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:001986
-name: cuttlefish and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:001987
-name: dairy barn
-is_a: OBT:001621 ! livestock barn
-
-[Term]
-id: OBT:001988
-name: dairy processing plant
-synonym: "dairy factory" EXACT []
-synonym: "milk processing factory" RELATED [TyDI:55159]
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:001989
-name: date and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:001990
-name: date palm tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:001991
-name: dead body
-is_a: OBT:001516 ! dead animal
-
-[Term]
-id: OBT:001992
-name: desiccation resistant
-synonym: "dessication resistant" RELATED [TyDI:56478]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:001993
-name: desiccation sensitive
-synonym: "dessication sensitive" RELATED [TyDI:56491]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:001994
-name: desiccation tolerant
-synonym: "dessication tolerant" RELATED [TyDI:56471]
-is_a: OBT:000137 ! phenotype wrt relative humidity impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:001995
-name: deteriorated canned food
-is_a: OBT:001473 ! canned food
-
-[Term]
-id: OBT:001996
-name: diadromous fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:001997
-name: disease resistant
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:001998
-name: disease sensitive
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:001999
-name: disease tolerant
-is_a: OBT:000125 ! phenotype wrt disease impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002000
-name: dough mixer
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002001
-name: dragee
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002002
-name: dried animal product
-is_a: OBT:001526 ! dried food
-
-[Term]
-id: OBT:002003
-name: dried bean
-is_a: OBT:001439 ! bean and related product
-
-[Term]
-id: OBT:002004
-name: dried lentil
-is_a: OBT:001617 ! lentil and related product
-
-[Term]
-id: OBT:002005
-name: dried pasta
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002006
-name: dried pea
-is_a: OBT:001696 ! pea and related product
-
-[Term]
-id: OBT:002007
-name: dried plant product
-is_a: OBT:001526 ! dried food
-
-[Term]
-id: OBT:002008
-name: dried seaweed
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:002009
-name: duck egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002010
-name: durian and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002011
-name: earthworm-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002012
-name: egg sac
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002013
-name: egg sac part
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002014
-name: embryo
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002015
-name: embryo part
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002016
-name: endosperm
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002017
-name: enriched dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002018
-name: environmental water with chemical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002019
-name: environmental water with physical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002020
-name: equine meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002021
-name: escarole and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002022
-name: ewe milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002023
-name: farmed fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002024
-name: fennel and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002025
-name: fermentation vat
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002026
-name: ferret
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002027
-name: fig and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:002028
-name: filarial nematode
-is_a: OBT:001693 ! parasitic nematode
-
-[Term]
-id: OBT:002029
-name: fir tree
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002030
-name: fish farming pond
-is_a: OBT:000046 ! aquaculture pond
-is_a: OBT:000093 ! fish pond
-
-[Term]
-id: OBT:002031
-name: fish sashimi
-synonym: "sashimi" RELATED [TyDI:54621]
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:002032
-name: fish-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002033
-name: flaxseed
-is_a: OBT:001551 ! flaxseed and primary derivative thereof
-
-[Term]
-id: OBT:002034
-name: flea
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002035
-name: flor
-synonym: "flor forming" EXACT [TyDI:50074]
-is_a: OBT:001444 ! biofilm forming
-
-[Term]
-id: OBT:002036
-name: fluvial dambo
-is_a: OBT:001513 ! dambo
-
-[Term]
-id: OBT:002037
-name: foie gras
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:002038
-name: folivorous bird
-synonym: "leaf-eating bird" EXACT [TyDI:56639]
-synonym: "leaves-eating bird" EXACT [TyDI:56640]
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002039
-name: food fermentation factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002040
-name: fork as utensil
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002041
-name: fowl
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002042
-name: fresh animal manure
-is_a: OBT:001416 ! animal manure
-
-[Term]
-id: OBT:002043
-name: fresh cheese
-is_a: OBT:001480 ! cheese
-
-[Term]
-id: OBT:002044
-name: fresh pasta
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002045
-name: freshwater fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002046
-name: freshwater sediment
-is_a: OBT:001430 ! aquatic sediment
-
-[Term]
-id: OBT:002047
-name: fried food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002048
-name: fried rice
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002049
-name: frikadeller
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002050
-name: frog product
-is_a: OBT:001404 ! amphibian and product thereof
-
-[Term]
-id: OBT:002051
-name: fruit fly
-synonym: "Drosophila" EXACT [TyDI:56449]
-is_a: OBT:001553 ! fly
-
-[Term]
-id: OBT:002052
-name: fruit salad
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:002053
-name: fruit smoothie
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:002054
-name: fruit-eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002055
-name: fungi as food
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002056
-name: game bird meat
-synonym: "bushmeat bird meat" EXACT [TyDI:54008]
-synonym: "wild feathered game" EXACT [TyDI:54009]
-is_a: OBT:001447 ! bird meat
-
-[Term]
-id: OBT:002057
-name: game mammal meat
-synonym: "wild meat" EXACT [TyDI:55569]
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002058
-name: garlic and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002059
-name: geese egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002060
-name: gherkin and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002061
-name: ginger and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002062
-name: glassy rind of seafloor basalt
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002063
-name: gnocchi
-is_a: OBT:001694 ! pasta and related product
-
-[Term]
-id: OBT:002064
-name: goat meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002065
-name: goat milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002066
-name: grape and primary derivative thereof
-synonym: "grape" EXACT [TyDI:51423]
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002067
-name: grape leaf and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002068
-name: griddled food
-synonym: "griddle cooked food" EXACT [TyDI:53310]
-synonym: "griddle-cooked food" EXACT [TyDI:53309]
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002069
-name: grilled food
-synonym: "barbecued food" EXACT [TyDI:52528]
-synonym: "broiled food" RELATED [TyDI:52529]
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002070
-name: gum drop
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002071
-name: hamburger
-is_a: OBT:001466 ! burger
-
-[Term]
-id: OBT:002072
-name: hard tick
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002073
-name: hay
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002074
-name: hazelnut
-is_a: OBT:001590 ! hazelnut and primary derivative thereof
-
-[Term]
-id: OBT:002075
-name: head cabbage and related product
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:002076
-name: hemp seed
-is_a: OBT:001593 ! hemp seed and primary derivative thereof
-
-[Term]
-id: OBT:002077
-name: hen egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002078
-name: herbivore
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002079
-name: high pressure treated food
-synonym: "high-pressure-treated food" RELATED [TyDI:53457]
-is_a: OBT:001729 ! pressure treated food
-
-[Term]
-id: OBT:002080
-name: honey bee
-is_a: OBT:001441 ! bee
-
-[Term]
-id: OBT:002081
-name: horseradish and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002082
-name: hospital equipment
-is_a: OBT:000097 ! hospital environment
-is_a: OBT:000108 ! medical equipment
-
-[Term]
-id: OBT:002083
-name: human milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002084
-name: ice tea
-is_a: OBT:001841 ! water based beverage
-
-[Term]
-id: OBT:002085
-name: ice-cream factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002086
-name: industrial bakery
-synonym: "bakery plant" EXACT [TyDI:54976]
-is_a: OBT:003759 ! bakery
-
-[Term]
-id: OBT:002087
-name: insect product
-is_a: OBT:001816 ! terrestrial invertebrate product
-
-[Term]
-id: OBT:002088
-name: integument
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002089
-name: jam
-is_a: OBT:001804 ! sugar-preserved food
-
-[Term]
-id: OBT:002090
-name: kaki and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:002091
-name: kiwi and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002092
-name: knife
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002093
-name: kombu
-is_a: OBT:001398 ! algae and related product
-
-[Term]
-id: OBT:002094
-name: kombucha
-is_a: OBT:001841 ! water based beverage
-
-[Term]
-id: OBT:002095
-name: lamb meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002096
-name: landfill leachate
-is_a: OBT:001680 ! organic leachate
-
-[Term]
-id: OBT:002097
-name: lasagna
-is_a: OBT:001695 ! pasta based dish
-
-[Term]
-id: OBT:002098
-name: laurel and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002099
-name: lavander and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002100
-name: lean dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002101
-name: leek and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002102
-name: left arm
-is_a: OBT:001432 ! arm
-
-[Term]
-id: OBT:002103
-name: lemon and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002104
-name: lentil
-is_a: OBT:001617 ! lentil and related product
-
-[Term]
-id: OBT:002105
-name: lettuce and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002106
-name: lime and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002107
-name: liqueur
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002108
-name: liquid egg mixed
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002109
-name: liquid egg white
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002110
-name: liquid egg yolk
-is_a: OBT:001619 ! liquid egg product
-
-[Term]
-id: OBT:002111
-name: litchi and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002112
-name: lizard product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002113
-name: lobster
-is_a: OBT:001630 ! marine crustacean
-
-[Term]
-id: OBT:002114
-name: lobster and product thereof
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:002115
-name: loukoumi
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002116
-name: louse
-synonym: "lice" EXACT [TyDI:50227]
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002117
-name: low salinity mud flat sediment
-is_a: OBT:001655 ! mud sediment
-
-[Term]
-id: OBT:002118
-name: lupin
-synonym: "lupine" EXACT [TyDI:51239]
-is_a: OBT:001622 ! lupin and related product
-
-[Term]
-id: OBT:002119
-name: lupin seed
-is_a: OBT:001622 ! lupin and related product
-
-[Term]
-id: OBT:002120
-name: maize and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002121
-name: mandarin and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002122
-name: mango and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002123
-name: mare milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002124
-name: marine anoxic mud
-is_a: OBT:001631 ! marine mud
-
-[Term]
-id: OBT:002125
-name: marine black mud
-is_a: OBT:001631 ! marine mud
-
-[Term]
-id: OBT:002126
-name: marine fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002127
-name: marine sediment
-synonym: "pelagic sediment \{alternative name\}" EXACT [TyDI:56108]
-is_a: OBT:001430 ! aquatic sediment
-
-[Term]
-id: OBT:002128
-name: marshmallow
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002129
-name: meat processing plant
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002130
-name: meat patty
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002131
-name: meat sashimi
-synonym: "sashimi" RELATED [TyDI:54621]
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002132
-name: melon and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002133
-name: merguez
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:002134
-name: micropyle
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002135
-name: mid-ocean ridge basalt
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002136
-name: milk product
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002137
-name: millet and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002138
-name: mint and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002139
-name: mixed vegetable
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:002140
-name: modified-atmosphere-packed food
-is_a: OBT:001687 ! packed food
-
-[Term]
-id: OBT:002141
-name: morel and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002142
-name: mosquito
-is_a: OBT:001453 ! blood-feeding insect
-
-[Term]
-id: OBT:002143
-name: moussaka
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002144
-name: mucocutaneous surface
-is_a: OBT:001654 ! mucosal surface
-
-[Term]
-id: OBT:002145
-name: mulberry tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002146
-name: mummy
-is_a: OBT:001516 ! dead animal
-
-[Term]
-id: OBT:002147
-name: mussel and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002148
-name: mustelidae
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002149
-name: mutton meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002150
-name: nectarine and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002151
-name: nougat
-is_a: OBT:001802 ! sugar confectionery
-
-[Term]
-id: OBT:002152
-name: nucellus
-is_a: OBT:001684 ! ovule part
-
-[Term]
-id: OBT:002153
-name: nutmeg
-synonym: "Myristica fragrans" EXACT [TyDI:54728]
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:002154
-name: oat and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002155
-name: octopus and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002156
-name: oil sludge
-is_a: OBT:001773 ! sludge
-
-[Term]
-id: OBT:002157
-name: okra and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002158
-name: oleander
-is_a: OBT:001771 ! shrub
-
-[Term]
-id: OBT:002159
-name: olive tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002160
-name: onion and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002161
-name: opossum
-synonym: "didelphidae" RELATED [TyDI:54144]
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002162
-name: orange and primary derivative thereof
-is_a: OBT:001487 ! citrus fruit and primary derivative thereof
-
-[Term]
-id: OBT:002163
-name: orange tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002164
-name: oregano and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002165
-name: oyster and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002166
-name: paella
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002167
-name: palm heart and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002168
-name: paper manufacture
-is_a: OBT:001626 ! manufacture
-
-[Term]
-id: OBT:002169
-name: parrot
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002170
-name: parsley and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002171
-name: parsnip and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002172
-name: passerine bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002173
-name: pasteurized food
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:002174
-name: pastry product
-synonym: "pastry" RELATED [TyDI:51162]
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:002175
-name: pea
-is_a: OBT:001696 ! pea and related product
-
-[Term]
-id: OBT:002176
-name: peach and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002177
-name: peanut as food
-is_a: OBT:001697 ! peanut and primary derivative thereof
-
-[Term]
-id: OBT:002178
-name: peanut butter
-is_a: OBT:001697 ! peanut and primary derivative thereof
-
-[Term]
-id: OBT:002179
-name: pear and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:002180
-name: pear tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002181
-name: pecan
-is_a: OBT:001701 ! pecan and primary derivative thereof
-
-[Term]
-id: OBT:002182
-name: pepper
-is_a: OBT:001784 ! spice
-
-[Term]
-id: OBT:002183
-name: phagocytosis resistant
-is_a: OBT:000131 ! phenotype wrt immune system impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002184
-name: pickled food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:002185
-name: pie
-is_a: OBT:001650 ! mixed dish
-
-[Term]
-id: OBT:002186
-name: pigeon
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002187
-name: pine
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002188
-name: pineapple and primary derivative thereof
-is_a: OBT:001569 ! fruit with inedible peel and primary derivative thereof
-
-[Term]
-id: OBT:002189
-name: pistachio
-is_a: OBT:001717 ! pistachio and primary derivative thereof
-
-[Term]
-id: OBT:002190
-name: plant cutting
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002191
-name: plum and primary derivative thereof
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-
-[Term]
-id: OBT:002192
-name: plum tree
-is_a: OBT:001567 ! fruit tree
-
-[Term]
-id: OBT:002193
-name: poached food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002194
-name: pollen
-is_a: OBT:001426 ! anther part
-
-[Term]
-id: OBT:002195
-name: poppy seed
-is_a: OBT:001723 ! poppy seed and primary derivative thereof
-
-[Term]
-id: OBT:002196
-name: pork
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002197
-name: potato and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002198
-name: poultry litter
-is_a: OBT:001620 ! litter
-
-[Term]
-id: OBT:002199
-name: poultry meat
-is_a: OBT:001447 ! bird meat
-
-[Term]
-id: OBT:002200
-name: prawn and product thereof
-synonym: "shrimp" RELATED [TyDI:56014]
-is_a: OBT:001508 ! crustacean and product thereof
-
-[Term]
-id: OBT:002201
-name: primate
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002202
-name: processed cheese
-is_a: OBT:001480 ! cheese
-
-[Term]
-id: OBT:002203
-name: public bathing facility
-is_a: OBT:000050 ! artificial water environment
-is_a: OBT:000145 ! public equipment
-
-[Term]
-id: OBT:002204
-name: pudding
-is_a: OBT:001650 ! mixed dish
-
-[Term]
-id: OBT:002205
-name: pumpkin and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002206
-name: pumpkin seed
-is_a: OBT:001731 ! pumpkin seed and primary derivative thereof
-
-[Term]
-id: OBT:002207
-name: quail egg
-is_a: OBT:001847 ! whole egg
-
-[Term]
-id: OBT:002208
-name: quince and primary derivative thereof
-is_a: OBT:001722 ! pome fruit and primary derivative thereof
-
-[Term]
-id: OBT:002209
-name: quinoa
-is_a: OBT:001734 ! quinoa and primary derivative thereof
-
-[Term]
-id: OBT:002210
-name: rabbit meat
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002211
-name: rabbit tick
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002212
-name: radiation resistant
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002213
-name: radiation sensitive
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:002214
-name: radiation tolerant
-is_a: OBT:000136 ! phenotype wrt radiation impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002215
-name: radish and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002216
-name: radish as food
-is_a: OBT:001459 ! brassica vegetable
-
-[Term]
-id: OBT:002217
-name: radish plant
-is_a: OBT:001391 ! Brassica
-
-[Term]
-id: OBT:002218
-name: raspberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002219
-name: ratatouille
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:002220
-name: redcurrant and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002221
-name: reheated food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002222
-name: rhubarb and related product
-is_a: OBT:001789 ! stem vegetable
-
-[Term]
-id: OBT:002223
-name: rice and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002224
-name: rice pudding
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:002225
-name: rice-plant residue
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002226
-name: right arm
-is_a: OBT:001432 ! arm
-
-[Term]
-id: OBT:002227
-name: ripened sausage
-is_a: OBT:001758 ! sausage
-
-[Term]
-id: OBT:002228
-name: roasted food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002229
-name: rocket and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002230
-name: rodent
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002231
-name: rosemary and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002232
-name: rum
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002233
-name: rye and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002234
-name: sage and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002235
-name: sake
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002236
-name: saline brine sediment
-is_a: OBT:001751 ! saline sediment
-
-[Term]
-id: OBT:002237
-name: salsify and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002238
-name: salted food
-is_a: OBT:001755 ! salt-preserved food
-
-[Term]
-id: OBT:002239
-name: sashimi
-is_a: OBT:001548 ! fish based dish
-
-[Term]
-id: OBT:002240
-name: scalded food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002241
-name: sea cucumber and product thereof
-is_a: OBT:001535 ! echinoderm and product thereof
-
-[Term]
-id: OBT:002242
-name: sea pineapple and product thereof
-synonym: "hoya" RELATED [TyDI:54865]
-synonym: "maboya" RELATED [TyDI:54864]
-synonym: "meongge" RELATED [TyDI:54863]
-is_a: OBT:001831 ! tunicate and product thereof
-
-[Term]
-id: OBT:002243
-name: sea salt
-is_a: OBT:001753 ! salt
-
-[Term]
-id: OBT:002244
-name: seed eating bird
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:002245
-name: sesame oil
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-
-[Term]
-id: OBT:002246
-name: sesame seed
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-
-[Term]
-id: OBT:002247
-name: shallot and related product
-is_a: OBT:001465 ! bulb vegetable
-
-[Term]
-id: OBT:002248
-name: sharpshooter
-is_a: OBT:001612 ! leafhopper
-
-[Term]
-id: OBT:002249
-name: simmered food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002250
-name: slash pine forest
-is_a: OBT:001715 ! pine forest
-
-[Term]
-id: OBT:002251
-name: slaughter plant
-synonym: "abattoir" RELATED [TyDI:50262]
-synonym: "slaughterhouse" EXACT [TyDI:50261]
-is_a: OBT:002129 ! meat processing plant
-
-[Term]
-id: OBT:002252
-name: slaughtering waste
-synonym: "abattoir waste" RELATED [TyDI:52683]
-is_a: OBT:001558 ! food processing waste
-
-[Term]
-id: OBT:002253
-name: snail product
-is_a: OBT:001816 ! terrestrial invertebrate product
-
-[Term]
-id: OBT:002254
-name: snake product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002255
-name: soap scum
-is_a: OBT:001618 ! lime soap
-
-[Term]
-id: OBT:002256
-name: soft tick
-synonym: "soft-bodied tick" EXACT [TyDI:50335]
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002257
-name: soil with chemical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:002258
-name: soil with physical property
-is_a: OBT:000009 ! habitat wrt chemico-physical property
-is_a: OBT:000427 ! soil
-
-[Term]
-id: OBT:002259
-name: soybean
-synonym: "soy" RELATED [TyDI:53483]
-synonym: "soya bean" RELATED [TyDI:53482]
-is_a: OBT:001781 ! soybean and related product
-
-[Term]
-id: OBT:002260
-name: spinach and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002261
-name: spirit
-is_a: OBT:001397 ! alcoholic drink
-
-[Term]
-id: OBT:002262
-name: spoon
-is_a: OBT:001509 ! cutlery
-
-[Term]
-id: OBT:002263
-name: spruce
-is_a: OBT:001498 ! conifer
-
-[Term]
-id: OBT:002264
-name: squid and product thereof
-is_a: OBT:001651 ! mollusc and product thereof
-
-[Term]
-id: OBT:002265
-name: stable manure
-is_a: OBT:001416 ! animal manure
-
-[Term]
-id: OBT:002266
-name: steak tartare
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:002267
-name: steamed food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002268
-name: sterilized food
-synonym: "sterilised food" EXACT [TyDI:52554]
-is_a: OBT:001592 ! heat-preserved food
-
-[Term]
-id: OBT:002269
-name: stewed food
-is_a: OBT:001499 ! cooked food
-
-[Term]
-id: OBT:002270
-name: storage box
-is_a: OBT:001556 ! food fermentation equipment
-
-[Term]
-id: OBT:002271
-name: straw
-is_a: OBT:001718 ! agricultural plant residue
-
-[Term]
-id: OBT:002272
-name: strawberry and primary derivative thereof
-is_a: OBT:001442 ! berry and small fruit and primary derivative thereof
-
-[Term]
-id: OBT:002273
-name: striploin
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002274
-name: submarine glassy basalt
-synonym: "submarine basalt glass" EXACT [TyDI:57953]
-is_a: OBT:001801 ! submarine basalt
-
-[Term]
-id: OBT:002275
-name: sugar factory
-is_a: OBT:001557 ! food processing factory
-
-[Term]
-id: OBT:002276
-name: sunflower seed
-is_a: OBT:001805 ! sunflower seed and primary derivatives thereof
-
-[Term]
-id: OBT:002277
-name: surimi
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002278
-name: swede and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002279
-name: sweet corn and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002280
-name: sweet dough
-is_a: OBT:001736 ! raw dough
-
-[Term]
-id: OBT:002281
-name: sweet pepper and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002282
-name: sweet potato and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002283
-name: tap water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:002284
-name: tarragon and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002285
-name: teff and primary derivative thereof
-synonym: "tef" EXACT [TyDI:51219]
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002286
-name: tenderloin
-is_a: OBT:001624 ! mammal meat
-
-[Term]
-id: OBT:002287
-name: testa
-synonym: "seed coat" RELATED [TyDI:56238]
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002288
-name: testa part
-is_a: OBT:001766 ! seed part
-
-[Term]
-id: OBT:002289
-name: thermal sensitive
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000153 ! stress sensitive
-
-[Term]
-id: OBT:002290
-name: thermal tolerant
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000154 ! stress tolerant
-
-[Term]
-id: OBT:002291
-name: thyme and related product
-synonym: "Thymus vulgaris" RELATED [TyDI:57449]
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002292
-name: tidal mudflat
-synonym: "intertidal mudflat" RELATED [TyDI:58218]
-synonym: "tidal flat" RELATED [TyDI:58217]
-is_a: OBT:001656 ! mudflat
-
-[Term]
-id: OBT:002293
-name: tomato and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002294
-name: tomato plant
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:002295
-name: triticale and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002296
-name: truffle and related product
-is_a: OBT:001573 ! fungi and related product
-
-[Term]
-id: OBT:002297
-name: turnip and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002298
-name: turtle product
-is_a: OBT:001742 ! reptile and product thereof
-
-[Term]
-id: OBT:002299
-name: urchin and product thereof
-is_a: OBT:001535 ! echinoderm and product thereof
-
-[Term]
-id: OBT:002300
-name: vacuum-packed food
-is_a: OBT:001687 ! packed food
-
-[Term]
-id: OBT:002301
-name: viennoiserie
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:002302
-name: walnut
-is_a: OBT:001838 ! walnut and primary derivative thereof
-
-[Term]
-id: OBT:002303
-name: walnut oil
-is_a: OBT:001838 ! walnut and primary derivative thereof
-
-[Term]
-id: OBT:002304
-name: wasabi and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002305
-name: watercress and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002306
-name: watermelon and related product
-is_a: OBT:001570 ! fruiting vegetable
-
-[Term]
-id: OBT:002307
-name: watermelon rind
-is_a: OBT:001566 ! fruit rind
-
-[Term]
-id: OBT:002308
-name: weatherfish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002309
-name: wheat and primary derivative thereof
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-
-[Term]
-id: OBT:002310
-name: white mustard and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002311
-name: wild fish meat
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:002312
-name: winter savory and related product
-is_a: OBT:001433 ! aromatic product and primary derivative thereof
-
-[Term]
-id: OBT:002313
-name: witloof and related product
-is_a: OBT:001613 ! leafy vegetable
-
-[Term]
-id: OBT:002314
-name: wood tick
-synonym: "American dog tick" EXACT [TyDI:54022]
-synonym: "Dermacentor variabilis" EXACT [TyDI:54020]
-synonym: "Ixodes ricinus" EXACT [TyDI:54021]
-is_a: OBT:001821 ! tick
-
-[Term]
-id: OBT:002315
-name: yak
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002316
-name: yak milk
-is_a: OBT:001645 ! milk
-
-[Term]
-id: OBT:002317
-name: yam and related product
-is_a: OBT:001747 ! root and tuber vegetable
-
-[Term]
-id: OBT:002318
-name: zebra
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:002319
-name: American cheese
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002320
-name: Cancoillotte
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002321
-name: Chinese cabbage
-is_a: OBT:001951 ! chinese cabbage and related product
-
-[Term]
-id: OBT:002322
-name: Crème de Brie de Meaux
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002323
-name: Danish pastry
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002324
-name: Drosophila melanogaster
-is_a: OBT:002051 ! fruit fly
-
-[Term]
-id: OBT:002325
-name: Kiri
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002326
-name: Knieküchle
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002327
-name: Ornithodoros moubata
-is_a: OBT:002256 ! soft tick
-
-[Term]
-id: OBT:002328
-name: Ornithodoros turicatae
-is_a: OBT:002256 ! soft tick
-
-[Term]
-id: OBT:002329
-name: The Laughing Cow
-synonym: "La Vache qui Rit" EXACT [TyDI:55418]
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002330
-name: UV radiation resistant
-synonym: "ultraviolet resistant" EXACT [TyDI:56250]
-synonym: "UV resistant" RELATED [TyDI:56251]
-is_a: OBT:002212 ! radiation resistant
-
-[Term]
-id: OBT:002331
-name: UV radiation sensitive
-synonym: "ultraviolet sensitive" EXACT [TyDI:50769]
-synonym: "UV sensitive" EXACT [TyDI:50768]
-is_a: OBT:002213 ! radiation sensitive
-
-[Term]
-id: OBT:002332
-name: UV radiation tolerant
-synonym: "ultraviolet tolerant" EXACT [TyDI:50773]
-synonym: "UV tolerant" EXACT [TyDI:50772]
-is_a: OBT:002214 ! radiation tolerant
-
-[Term]
-id: OBT:002333
-name: Vienna bread
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002334
-name: anchovie meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002335
-name: anglerfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002336
-name: animal filarial nematode
-is_a: OBT:002028 ! filarial nematode
-
-[Term]
-id: OBT:002337
-name: antimicrobial resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002338
-name: antimicrobial sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002339
-name: antimicrobial tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000378 ! phenotype wrt antimicrobial impact
-
-[Term]
-id: OBT:002340
-name: aphotic zone
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002341
-name: apple as food
-synonym: "apple" EXACT [TyDI:50312]
-is_a: OBT:001879 ! apple and primary derivative thereof
-
-[Term]
-id: OBT:002342
-name: apricot as food
-synonym: "apricot" EXACT [TyDI:50271]
-is_a: OBT:001881 ! apricot and primary derivative thereof
-
-[Term]
-id: OBT:002343
-name: arable soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002344
-name: arctic marine sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002345
-name: artichoke
-is_a: OBT:001883 ! artichoke and related product
-
-[Term]
-id: OBT:002346
-name: asparagus
-is_a: OBT:001885 ! aspargus and related product
-
-[Term]
-id: OBT:002347
-name: aubergine
-is_a: OBT:001886 ! aubergine and related product
-
-[Term]
-id: OBT:002348
-name: avocado as food
-synonym: "avocado" EXACT [TyDI:50236]
-is_a: OBT:001887 ! avocado and primary derivative thereof
-
-[Term]
-id: OBT:002349
-name: baboon
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002350
-name: baby corn
-is_a: OBT:001888 ! baby corn and related product
-
-[Term]
-id: OBT:002351
-name: bacon
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002352
-name: bamboo shoot
-is_a: OBT:001890 ! bamboo shoot and related product
-
-[Term]
-id: OBT:002353
-name: banana as food
-synonym: "banana" EXACT [TyDI:50244]
-is_a: OBT:001891 ! banana and primary derivative thereof
-
-[Term]
-id: OBT:002354
-name: barb meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002355
-name: barley product
-is_a: OBT:001893 ! barley and primary derivative thereof
-
-[Term]
-id: OBT:002356
-name: barracuda meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002357
-name: basil
-is_a: OBT:001894 ! basil and related product
-
-[Term]
-id: OBT:002358
-name: beaver
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002359
-name: beefsteak
-synonym: "beef steak" EXACT [TyDI:53992]
-synonym: "steak" RELATED [TyDI:53991]
-is_a: OBT:001899 ! beef
-
-[Term]
-id: OBT:002360
-name: beer-bottling plant
-is_a: OBT:001910 ! bottling factory
-
-[Term]
-id: OBT:002361
-name: beetroot
-is_a: OBT:001900 ! beetroot and related product
-
-[Term]
-id: OBT:002362
-name: berry as food
-synonym: "berry" EXACT [TyDI:54527]
-is_a: OBT:001901 ! berry and primary derivative thereof
-
-[Term]
-id: OBT:002363
-name: bison meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002364
-name: black anoxic marine sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002365
-name: black pepper
-is_a: OBT:002182 ! pepper
-
-[Term]
-id: OBT:002366
-name: black pudding
-is_a: OBT:001906 ! blood sausage
-
-[Term]
-id: OBT:002367
-name: blackberry as food
-synonym: "blackberry" EXACT [TyDI:50341]
-is_a: OBT:001903 ! blackberry and primary derivative thereof
-
-[Term]
-id: OBT:002368
-name: blackcurrant as food
-synonym: "blackcurrant" EXACT [TyDI:54518]
-is_a: OBT:001904 ! blackcurrant and primary derivative thereof
-
-[Term]
-id: OBT:002369
-name: blueberry as food
-synonym: "blueberry" EXACT [TyDI:51062]
-is_a: OBT:001907 ! blueberry and primary derivative thereof
-
-[Term]
-id: OBT:002370
-name: bonito meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002371
-name: brackish water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002372
-name: brewery
-is_a: OBT:002039 ! food fermentation factory
-
-[Term]
-id: OBT:002373
-name: brioche
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002374
-name: broccoli
-is_a: OBT:001915 ! broccoli and related product
-
-[Term]
-id: OBT:002375
-name: brussel sprout as food
-synonym: "brussel sprout" RELATED [TyDI:53198]
-is_a: OBT:001916 ! brussel sprout and related product
-
-[Term]
-id: OBT:002376
-name: buegill sunfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002377
-name: burnt soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002378
-name: calcareous ooze
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002379
-name: carbonated bottled water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002380
-name: cardoon
-is_a: OBT:001933 ! cardoon and related product
-
-[Term]
-id: OBT:002381
-name: carp meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002382
-name: carrot
-is_a: OBT:001934 ! carrot and related product
-
-[Term]
-id: OBT:002383
-name: catfish meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002384
-name: cauliflower as food
-is_a: OBT:001937 ! cauliflower and related product
-
-[Term]
-id: OBT:002385
-name: celeriac
-is_a: OBT:001938 ! celeriac and related product
-
-[Term]
-id: OBT:002386
-name: celery
-is_a: OBT:001939 ! celery and related product
-
-[Term]
-id: OBT:002387
-name: celery leaf
-is_a: OBT:001940 ! celery leaf and related product
-
-[Term]
-id: OBT:002388
-name: chard
-is_a: OBT:001943 ! chard and related product
-
-[Term]
-id: OBT:002389
-name: chemically stressed soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002390
-name: chemocline
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002391
-name: cherry as food
-synonym: "cherry" EXACT [TyDI:50286]
-is_a: OBT:001946 ! cherry and primary derivative thereof
-
-[Term]
-id: OBT:002392
-name: cherry tomato
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002393
-name: chhena
-synonym: "chhana" EXACT [TyDI:55480]
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002394
-name: chicken meat
-synonym: "broiler meat" RELATED [TyDI:54389]
-synonym: "chicken" RELATED [TyDI:53594]
-synonym: "retailed chicken" RELATED [TyDI:54390]
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002395
-name: chili pepper
-synonym: "chile pepper" EXACT [TyDI:50029]
-synonym: "chilli" EXACT [TyDI:50031]
-synonym: "chilli pepper" EXACT [TyDI:50030]
-is_a: OBT:001950 ! chili pepper and related product
-
-[Term]
-id: OBT:002396
-name: chimpanzee
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002397
-name: chinchilla
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002398
-name: chive
-is_a: OBT:001953 ! chive and related product
-
-[Term]
-id: OBT:002399
-name: citronella grass
-synonym: "Cymbopogon nardus" EXACT [TyDI:54096]
-is_a: OBT:001955 ! citronella grass and related product
-
-[Term]
-id: OBT:002400
-name: clove
-is_a: OBT:001957 ! clove and related product
-
-[Term]
-id: OBT:002401
-name: coarse beach sand
-is_a: OBT:001896 ! beach sand
-
-[Term]
-id: OBT:002402
-name: coastal sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002403
-name: cod meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002404
-name: cold sensitive
-synonym: "low temperature sensitive" RELATED [TyDI:51159]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002405
-name: cold soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002406
-name: cold tolerant
-synonym: "low temperature tolerant" RELATED [TyDI:51138]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002407
-name: cool soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002408
-name: cottage cheese
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002409
-name: cotyledon
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002410
-name: courgette
-is_a: OBT:001972 ! courgette and related product
-
-[Term]
-id: OBT:002411
-name: crab as food
-is_a: OBT:001977 ! crab and product thereof
-
-[Term]
-id: OBT:002412
-name: cranberry as food
-is_a: OBT:001979 ! cranberry and primary derivative thereof
-
-[Term]
-id: OBT:002413
-name: cream pastry
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002414
-name: creamery
-is_a: OBT:001988 ! dairy processing plant
-
-[Term]
-id: OBT:002415
-name: creek sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002416
-name: croissant
-is_a: OBT:002301 ! viennoiserie
-
-[Term]
-id: OBT:002417
-name: crusty bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002418
-name: cucumber
-is_a: OBT:001981 ! cucumber and related product
-
-[Term]
-id: OBT:002419
-name: date as food
-synonym: "date" EXACT [TyDI:50268]
-is_a: OBT:001989 ! date and primary derivative thereof
-
-[Term]
-id: OBT:002420
-name: deep-sea sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002421
-name: deer meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002422
-name: deer tick
-synonym: "Ixodes scapularis" EXACT [TyDI:52581]
-is_a: OBT:002072 ! hard tick
-
-[Term]
-id: OBT:002423
-name: ditch sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002424
-name: dog tick
-is_a: OBT:002072 ! hard tick
-
-[Term]
-id: OBT:002425
-name: dolphinfish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002426
-name: dry soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002427
-name: duck meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002428
-name: durian as food
-synonym: "durian" EXACT [TyDI:55310]
-is_a: OBT:002010 ! durian and primary derivative thereof
-
-[Term]
-id: OBT:002429
-name: eel meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002430
-name: egg cell
-is_a: OBT:002013 ! egg sac part
-
-[Term]
-id: OBT:002431
-name: elk meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002432
-name: embryonic axis
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002433
-name: embryonic axis part
-is_a: OBT:002015 ! embryo part
-
-[Term]
-id: OBT:002434
-name: emperor meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002435
-name: enriched bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002436
-name: enriched soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002437
-name: erythrocyte
-synonym: "red blood cell" EXACT [TyDI:54125]
-is_a: OBT:000061 ! cell
-is_a: OBT:000231 ! circulatory system part
-
-[Term]
-id: OBT:002438
-name: escarole
-is_a: OBT:002021 ! escarole and related product
-
-[Term]
-id: OBT:002439
-name: eutrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002440
-name: extreme cold sensitive
-synonym: "extreme low temperature sensitive" RELATED [TyDI:51086]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002441
-name: extreme cold tolerant
-synonym: "extreme low temperature tolerant" RELATED [TyDI:51150]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002442
-name: extreme heat sensitive
-synonym: "extreme high temperature sensitive" RELATED [TyDI:51107]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002443
-name: extreme heat tolerant
-synonym: "extreme high temperature tolerant" RELATED [TyDI:51145]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002444
-name: fennel
-is_a: OBT:002024 ! fennel and related product
-
-[Term]
-id: OBT:002445
-name: field soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002446
-name: fig as food
-synonym: "fig" EXACT [TyDI:50255]
-is_a: OBT:002027 ! fig and primary derivative thereof
-
-[Term]
-id: OBT:002447
-name: filtered tap water
-is_a: OBT:002283 ! tap water
-
-[Term]
-id: OBT:002448
-name: finch
-is_a: OBT:002172 ! passerine bird
-
-[Term]
-id: OBT:002449
-name: flavoured water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002450
-name: flouder meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002451
-name: footwarm bath
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002452
-name: forest pond sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002453
-name: freeze-thaw sensitive
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002454
-name: freeze-thaw tolerant
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002455
-name: freshwater
-synonym: "fresh water" EXACT [TyDI:55545]
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002456
-name: freshwater bream meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002457
-name: frog leg
-is_a: OBT:002050 ! frog product
-
-[Term]
-id: OBT:002458
-name: frozen soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002459
-name: gamefowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002460
-name: garlic as food
-is_a: OBT:002058 ! garlic and related product
-
-[Term]
-id: OBT:002461
-name: gherkin
-is_a: OBT:002060 ! gherkin and related product
-
-[Term]
-id: OBT:002462
-name: gluten-free bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002463
-name: goose meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002464
-name: grape leaf
-is_a: OBT:002067 ! grape leaf and related product
-
-[Term]
-id: OBT:002465
-name: greenhouse soil
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002466
-name: ground beef
-is_a: OBT:001899 ! beef
-
-[Term]
-id: OBT:002467
-name: ground water
-synonym: "groundwater" EXACT [TyDI:58276]
-synonym: "subterranean water" RELATED [TyDI:58277]
-synonym: "underground water" EXACT [TyDI:58278]
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:000269 ! environment water
-
-[Term]
-id: OBT:002468
-name: groundwater body
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:000326 ! inland water body
-
-[Term]
-id: OBT:002469
-name: guinea fowl meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002470
-name: guinea pig
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002471
-name: haddock meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002472
-name: hake meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002473
-name: halibut meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002474
-name: ham
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002475
-name: hamster
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002476
-name: hare meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002477
-name: head cabbage
-synonym: "cabbage" RELATED [TyDI:53192]
-is_a: OBT:002075 ! head cabbage and related product
-
-[Term]
-id: OBT:002478
-name: heat sensitive
-synonym: "high temperature sensitive" RELATED [TyDI:50722]
-is_a: OBT:002289 ! thermal sensitive
-
-[Term]
-id: OBT:002479
-name: heat stressed soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002480
-name: heat tolerant
-synonym: "high temperature tolerant" RELATED [TyDI:51156]
-is_a: OBT:002290 ! thermal tolerant
-
-[Term]
-id: OBT:002481
-name: herring emat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002482
-name: hilum
-is_a: OBT:002288 ! testa part
-
-[Term]
-id: OBT:002483
-name: horseradish
-is_a: OBT:002081 ! horseradish and related product
-
-[Term]
-id: OBT:002484
-name: hospital bed
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002485
-name: hospital nebulizer
-synonym: "hospital nebuliser" EXACT [TyDI:55172]
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002486
-name: hospital water supply
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002487
-name: hot tap water
-is_a: OBT:002283 ! tap water
-
-[Term]
-id: OBT:002488
-name: human
-synonym: "homo sapiens" EXACT [TyDI:52730]
-synonym: "individual" RELATED [TyDI:52728]
-synonym: "people" RELATED [TyDI:52731]
-synonym: "person" RELATED [TyDI:52727]
-synonym: "subject" EXACT [TyDI:52729]
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:002489
-name: human filarial nematode
-is_a: OBT:002028 ! filarial nematode
-
-[Term]
-id: OBT:002490
-name: human louse
-synonym: "Pediculus humanus" EXACT [TyDI:54240]
-is_a: OBT:002116 ! louse
-
-[Term]
-id: OBT:002491
-name: hyper saline brine sediment
-synonym: "highly saline brine" RELATED [TyDI:54301]
-is_a: OBT:002236 ! saline brine sediment
-
-[Term]
-id: OBT:002492
-name: ionizing radiation resistant
-is_a: OBT:002212 ! radiation resistant
-
-[Term]
-id: OBT:002493
-name: ionizing radiation sensitive
-is_a: OBT:002213 ! radiation sensitive
-
-[Term]
-id: OBT:002494
-name: ionizing radiation tolerant
-is_a: OBT:002214 ! radiation tolerant
-
-[Term]
-id: OBT:002495
-name: jacuzzi
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002496
-name: kaki as food
-synonym: "kaki" EXACT [TyDI:50258]
-is_a: OBT:002090 ! kaki and primary derivative thereof
-
-[Term]
-id: OBT:002497
-name: kangaroo
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002498
-name: kiwi as food
-synonym: "kiwi" EXACT [TyDI:50265]
-is_a: OBT:002091 ! kiwi and primary derivative thereof
-
-[Term]
-id: OBT:002499
-name: lake sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002500
-name: landfowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002501
-name: laurel
-is_a: OBT:002098 ! laurel and related product
-
-[Term]
-id: OBT:002502
-name: lavander
-synonym: "lavandula augustifolia" EXACT [TyDI:54151]
-is_a: OBT:002099 ! lavander and related product
-
-[Term]
-id: OBT:002503
-name: leavened bread
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:002504
-name: leek
-is_a: OBT:002101 ! leek and related product
-
-[Term]
-id: OBT:002505
-name: lemon as food
-synonym: "lemon" EXACT [TyDI:50315]
-is_a: OBT:002103 ! lemon and primary derivative thereof
-
-[Term]
-id: OBT:002506
-name: lettuce
-is_a: OBT:002105 ! lettuce and related product
-
-[Term]
-id: OBT:002507
-name: lime as food
-synonym: "lime" EXACT [TyDI:50292]
-is_a: OBT:002106 ! lime and primary derivative thereof
-
-[Term]
-id: OBT:002508
-name: litchi as food
-synonym: "litchi" EXACT [TyDI:50252]
-is_a: OBT:002111 ! litchi and primary derivative thereof
-
-[Term]
-id: OBT:002509
-name: lobster as food
-is_a: OBT:002114 ! lobster and product thereof
-
-[Term]
-id: OBT:002510
-name: louse-born
-is_a: OBT:002116 ! louse
-
-[Term]
-id: OBT:002511
-name: low nutrient aquatic habitat
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002512
-name: mackerel meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002513
-name: maize
-synonym: "corn" NARROW []
-is_a: OBT:002120 ! maize and primary derivative thereof
-
-[Term]
-id: OBT:002514
-name: mandarin as food
-synonym: "mandarin" EXACT [TyDI:50309]
-is_a: OBT:002121 ! mandarin and primary derivative thereof
-
-[Term]
-id: OBT:002515
-name: mango as food
-synonym: "mango" EXACT [TyDI:50247]
-is_a: OBT:002122 ! mango and primary derivative thereof
-
-[Term]
-id: OBT:002516
-name: marine marsh sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002517
-name: marine sulfidic sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002518
-name: medical center
-is_a: OBT:000011 ! medical environment
-is_a: OBT:000963 ! welfare center
-
-[Term]
-id: OBT:002519
-name: melon as food
-is_a: OBT:002132 ! melon and related product
-
-[Term]
-id: OBT:002520
-name: mesotrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002521
-name: metal resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002522
-name: metal sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002523
-name: metal tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000384 ! phenotype wrt metal concentration impact
-
-[Term]
-id: OBT:002524
-name: milk rice
-synonym: "kiribath" EXACT [TyDI:57336]
-is_a: OBT:002224 ! rice pudding
-
-[Term]
-id: OBT:002525
-name: millet
-is_a: OBT:002137 ! millet and primary derivative thereof
-
-[Term]
-id: OBT:002526
-name: mineral water
-is_a: OBT:001909 ! bottled water
-
-[Term]
-id: OBT:002527
-name: mink
-is_a: OBT:002148 ! mustelidae
-
-[Term]
-id: OBT:002528
-name: mint
-is_a: OBT:002138 ! mint and related product
-
-[Term]
-id: OBT:002529
-name: mullet meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002530
-name: murine
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002531
-name: mushroom bed
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002532
-name: muskrat
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002533
-name: nectarine as food
-synonym: "nectarine" EXACT [TyDI:50279]
-is_a: OBT:002150 ! nectarine and primary derivative thereof
-
-[Term]
-id: OBT:002534
-name: nitrogen-poor soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002535
-name: nutrient-poor soil
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:002536
-name: oat as food
-is_a: OBT:002154 ! oat and primary derivative thereof
-
-[Term]
-id: OBT:002537
-name: okra
-is_a: OBT:002157 ! okra and related product
-
-[Term]
-id: OBT:002538
-name: oligotrophic water
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002539
-name: onion
-is_a: OBT:002160 ! onion and related product
-
-[Term]
-id: OBT:002540
-name: orange as food
-synonym: "orange" EXACT [TyDI:50320]
-is_a: OBT:002162 ! orange and primary derivative thereof
-
-[Term]
-id: OBT:002541
-name: oregano
-synonym: "Origanum vulgare" EXACT [TyDI:55299]
-is_a: OBT:002164 ! oregano and related product
-
-[Term]
-id: OBT:002542
-name: paddle fish meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002543
-name: palm heart
-is_a: OBT:002167 ! palm heart and related product
-
-[Term]
-id: OBT:002544
-name: parakeet
-is_a: OBT:002169 ! parrot
-
-[Term]
-id: OBT:002545
-name: parsley
-is_a: OBT:002170 ! parsley and related product
-
-[Term]
-id: OBT:002546
-name: parsnip
-is_a: OBT:002171 ! parsnip and related product
-
-[Term]
-id: OBT:002547
-name: peach as food
-synonym: "peach" EXACT [TyDI:50289]
-is_a: OBT:002176 ! peach and primary derivative thereof
-
-[Term]
-id: OBT:002548
-name: pear as food
-synonym: "pear" EXACT [TyDI:50303]
-is_a: OBT:002179 ! pear and primary derivative thereof
-
-[Term]
-id: OBT:002549
-name: pear tomato
-synonym: "corn seed" RELATED [TyDI:54233]
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002550
-name: perch meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002551
-name: permafrost
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002552
-name: pheasant meat
-is_a: OBT:002056 ! game bird meat
-
-[Term]
-id: OBT:002553
-name: photic zone
-synonym: "euphotic zone" RELATED [TyDI:54119]
-synonym: "illuminated aquatic environment" RELATED [TyDI:54120]
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002554
-name: pickles
-is_a: OBT:002184 ! pickled food
-
-[Term]
-id: OBT:002555
-name: pico de gallo
-is_a: OBT:002139 ! mixed vegetable
-
-[Term]
-id: OBT:002556
-name: pig's trotter
-synonym: "pettitoe" RELATED [TyDI:55977]
-is_a: OBT:001866 ! animal foot
-
-[Term]
-id: OBT:002557
-name: pigeon meat
-is_a: OBT:002056 ! game bird meat
-
-[Term]
-id: OBT:002558
-name: pineapple as food
-synonym: "pineapple" EXACT [TyDI:50239]
-is_a: OBT:002188 ! pineapple and primary derivative thereof
-
-[Term]
-id: OBT:002559
-name: plum tomato
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002560
-name: pork chop
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002561
-name: potato as food
-is_a: OBT:002197 ! potato and related product
-
-[Term]
-id: OBT:002562
-name: poultry deep litter
-is_a: OBT:002198 ! poultry litter
-
-[Term]
-id: OBT:002563
-name: prawn
-synonym: "shrimp" RELATED [TyDI:56014]
-is_a: OBT:002200 ! prawn and product thereof
-
-[Term]
-id: OBT:002564
-name: public sauna
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002565
-name: puff pastry
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:002566
-name: pumpkin
-is_a: OBT:002205 ! pumpkin and related product
-
-[Term]
-id: OBT:002567
-name: quail meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002568
-name: quark
-synonym: "quarg" EXACT [TyDI:55435]
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002569
-name: queso blanco
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002570
-name: queso fresco
-is_a: OBT:002043 ! fresh cheese
-
-[Term]
-id: OBT:002571
-name: quince as food
-synonym: "quince" EXACT [TyDI:50306]
-is_a: OBT:002208 ! quince and primary derivative thereof
-
-[Term]
-id: OBT:002572
-name: rabbit
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002573
-name: radish
-is_a: OBT:002215 ! radish and related product
-
-[Term]
-id: OBT:002574
-name: raspberry as food
-synonym: "raspberry" EXACT [TyDI:50787]
-is_a: OBT:002218 ! raspberry and primary derivative thereof
-
-[Term]
-id: OBT:002575
-name: rat flea
-is_a: OBT:002034 ! flea
-
-[Term]
-id: OBT:002576
-name: ratite meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002577
-name: ray meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002578
-name: redcurrant as food
-synonym: "redcurrant" EXACT [TyDI:54515]
-is_a: OBT:002220 ! redcurrant and primary derivative thereof
-
-[Term]
-id: OBT:002579
-name: rhubarb
-is_a: OBT:002222 ! rhubarb and related product
-
-[Term]
-id: OBT:002580
-name: rice
-is_a: OBT:002223 ! rice and primary derivative thereof
-
-[Term]
-id: OBT:002581
-name: rice paddy
-synonym: "rice field" RELATED [TyDI:56094]
-synonym: "rice paddies" EXACT [TyDI:56095]
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002582
-name: rice straw
-is_a: OBT:002271 ! straw
-
-[Term]
-id: OBT:002583
-name: rice waste
-is_a: OBT:002225 ! rice-plant residue
-
-[Term]
-id: OBT:002584
-name: rice-straw residue
-is_a: OBT:002225 ! rice-plant residue
-
-[Term]
-id: OBT:002585
-name: river sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002586
-name: roach meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002587
-name: rocket
-is_a: OBT:002229 ! rocket and related product
-
-[Term]
-id: OBT:002588
-name: rosemary
-is_a: OBT:002231 ! rosemary and related product
-
-[Term]
-id: OBT:002589
-name: ruminant
-synonym: "ruminant livestock" EXACT [TyDI:52724]
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002590
-name: rye
-is_a: OBT:002233 ! rye and primary derivative thereof
-
-[Term]
-id: OBT:002591
-name: sage
-is_a: OBT:002234 ! sage and related product
-
-[Term]
-id: OBT:002592
-name: saline water
-synonym: "salt water" EXACT [TyDI:58269]
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002593
-name: salmon meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002594
-name: salsify
-is_a: OBT:002237 ! salsify and related product
-
-[Term]
-id: OBT:002595
-name: salt pork
-is_a: OBT:002196 ! pork
-
-[Term]
-id: OBT:002596
-name: sardine meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002597
-name: shad meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002598
-name: shallot
-is_a: OBT:002247 ! shallot and related product
-
-[Term]
-id: OBT:002599
-name: shark meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002600
-name: siliceous ooze
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002601
-name: smelt meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002602
-name: sole meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002603
-name: spa
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002604
-name: spinach
-is_a: OBT:002260 ! spinach and related product
-
-[Term]
-id: OBT:002605
-name: spring sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002606
-name: squirrel
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002607
-name: strawberry as food
-synonym: "strawberry" EXACT [TyDI:50300]
-is_a: OBT:002272 ! strawberry and primary derivative thereof
-
-[Term]
-id: OBT:002608
-name: stream sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002609
-name: sturgeon meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002610
-name: sugar cane field
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002611
-name: sulfide-rich freshwater sediment
-is_a: OBT:002046 ! freshwater sediment
-
-[Term]
-id: OBT:002612
-name: sulfidic coastal sediment
-is_a: OBT:002127 ! marine sediment
-
-[Term]
-id: OBT:002613
-name: surgery
-synonym: "surgical" RELATED [TyDI:50859]
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002614
-name: surgical device
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:002615
-name: swede
-is_a: OBT:002278 ! swede and related product
-
-[Term]
-id: OBT:002616
-name: sweet corn
-is_a: OBT:002279 ! sweet corn and related product
-
-[Term]
-id: OBT:002617
-name: sweet pepper
-is_a: OBT:002281 ! sweet pepper and related product
-
-[Term]
-id: OBT:002618
-name: sweet potato
-is_a: OBT:002282 ! sweet potato and related product
-
-[Term]
-id: OBT:002619
-name: swimming pool
-is_a: OBT:002203 ! public bathing facility
-
-[Term]
-id: OBT:002620
-name: table grape as food
-synonym: "grape" RELATED [TyDI:51423]
-synonym: "table grape" EXACT [TyDI:55471]
-is_a: OBT:002066 ! grape and primary derivative thereof
-
-[Term]
-id: OBT:002621
-name: tarragon
-is_a: OBT:002284 ! tarragon and related product
-
-[Term]
-id: OBT:002622
-name: teff
-is_a: OBT:002285 ! teff and primary derivative thereof
-
-[Term]
-id: OBT:002623
-name: thyme
-is_a: OBT:002291 ! thyme and related product
-
-[Term]
-id: OBT:002624
-name: tilapia meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002625
-name: tomato as food
-is_a: OBT:002293 ! tomato and related product
-
-[Term]
-id: OBT:002626
-name: triticale
-is_a: OBT:002295 ! triticale and primary derivative thereof
-
-[Term]
-id: OBT:002627
-name: tropical soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002628
-name: trout meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002629
-name: tuna meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002630
-name: turbot meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002631
-name: turkey meat
-is_a: OBT:002199 ! poultry meat
-
-[Term]
-id: OBT:002632
-name: turnip
-is_a: OBT:002297 ! turnip and related product
-
-[Term]
-id: OBT:002633
-name: velveeta
-is_a: OBT:002202 ! processed cheese
-
-[Term]
-id: OBT:002634
-name: venison meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002635
-name: vole
-is_a: OBT:002230 ! rodent
-
-[Term]
-id: OBT:002636
-name: waffle mixture
-is_a: OBT:002280 ! sweet dough
-
-[Term]
-id: OBT:002637
-name: wasabi
-is_a: OBT:002304 ! wasabi and related product
-
-[Term]
-id: OBT:002638
-name: water-stressed soil
-is_a: OBT:002258 ! soil with physical property
-
-[Term]
-id: OBT:002639
-name: watercress
-is_a: OBT:002305 ! watercress and related product
-
-[Term]
-id: OBT:002640
-name: waterfowl
-is_a: OBT:002041 ! fowl
-
-[Term]
-id: OBT:002641
-name: watermelon as food
-is_a: OBT:002306 ! watermelon and related product
-
-[Term]
-id: OBT:002642
-name: wheat field
-is_a: OBT:001982 ! cultivated field
-
-[Term]
-id: OBT:002643
-name: wheat product
-is_a: OBT:002309 ! wheat and primary derivative thereof
-
-[Term]
-id: OBT:002644
-name: wheat semolina
-synonym: "semolina" RELATED [TyDI:54912]
-is_a: OBT:002309 ! wheat and primary derivative thereof
-
-[Term]
-id: OBT:002645
-name: white mustard
-synonym: "Brassica hirta" EXACT [TyDI:54090]
-is_a: OBT:002310 ! white mustard and related product
-
-[Term]
-id: OBT:002646
-name: white pepper
-is_a: OBT:002182 ! pepper
-
-[Term]
-id: OBT:002647
-name: whitefish meat
-is_a: OBT:001996 ! diadromous fish meat
-
-[Term]
-id: OBT:002648
-name: wild boar meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002649
-name: wild rabbit meat
-is_a: OBT:002057 ! game mammal meat
-
-[Term]
-id: OBT:002650
-name: wine grape as food
-synonym: "wine grape" EXACT [TyDI:50297]
-is_a: OBT:002066 ! grape and primary derivative thereof
-
-[Term]
-id: OBT:002651
-name: winter savory
-synonym: "Satureja montana" EXACT [TyDI:54093]
-is_a: OBT:002312 ! winter savory and related product
-
-[Term]
-id: OBT:002652
-name: witloof
-is_a: OBT:002313 ! witloof and related product
-
-[Term]
-id: OBT:002653
-name: wolffish meat
-is_a: OBT:002126 ! marine fish meat
-
-[Term]
-id: OBT:002654
-name: wombat
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:002655
-name: wuchang bream meat
-is_a: OBT:002045 ! freshwater fish meat
-
-[Term]
-id: OBT:002656
-name: yam
-is_a: OBT:002317 ! yam and related product
-
-[Term]
-id: OBT:002657
-name: yeast
-is_a: OBT:000114 ! microorganism
-is_a: OBT:000290 ! fungi
-
-[Term]
-id: OBT:002658
-name: Brugia malayi
-is_a: OBT:002489 ! human filarial nematode
-
-[Term]
-id: OBT:002659
-name: UVA radiation resistant
-synonym: "UV-A radiation resistant" EXACT [TyDI:56244]
-synonym: "UV-A resistant" EXACT [TyDI:56243]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002660
-name: UVA radiation sensitive
-synonym: "UV-A radiation sensitive" EXACT [TyDI:56276]
-synonym: "UV-A sensitive" EXACT [TyDI:56275]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002661
-name: UVA radiation tolerant
-synonym: "UV-A radiation tolerant" EXACT [TyDI:50781]
-synonym: "UV-A tolerant" EXACT [TyDI:50780]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002662
-name: UVB radiation resistant
-synonym: "UV-B radiation resistant" EXACT [TyDI:56304]
-synonym: "UV-B resistant" EXACT [TyDI:56303]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002663
-name: UVB radiation sensitive
-synonym: "UV-B radiation sensitive" EXACT [TyDI:56267]
-synonym: "UV-B sensitive" EXACT [TyDI:56268]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002664
-name: UVB radiation tolerant
-synonym: "UV-B radiation tolerant" EXACT [TyDI:50764]
-synonym: "UV-B tolerant" EXACT [TyDI:50765]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002665
-name: UVC radiation resistant
-synonym: "UV-C radiation resistant" EXACT [TyDI:56312]
-synonym: "UV-C resistant" EXACT [TyDI:56311]
-is_a: OBT:002330 ! UV radiation resistant
-
-[Term]
-id: OBT:002666
-name: UVC radiation sensitive
-synonym: "UV-C radiation sensitive" EXACT [TyDI:56288]
-synonym: "UV-C sensitive" EXACT [TyDI:56287]
-is_a: OBT:002331 ! UV radiation sensitive
-
-[Term]
-id: OBT:002667
-name: UVC radiation tolerant
-synonym: "UV-C radiation tolerant" EXACT [TyDI:50759]
-synonym: "UV-C tolerant" EXACT [TyDI:50758]
-is_a: OBT:002332 ! UV radiation tolerant
-
-[Term]
-id: OBT:002668
-name: animal commensal
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000239 ! commensal
-
-[Term]
-id: OBT:002669
-name: animal pathogen
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000375 ! pathogen
-
-[Term]
-id: OBT:002670
-name: anoxic river sediment
-is_a: OBT:002585 ! river sediment
-
-[Term]
-id: OBT:002671
-name: antibacterial resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002672
-name: antibacterial sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002673
-name: antibacterial tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002674
-name: antibiotic resistant
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:000598 ! drug resistant
-
-[Term]
-id: OBT:002675
-name: antibiotic sensitive
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:000599 ! drug sensitive
-
-[Term]
-id: OBT:002676
-name: antibiotic tolerant
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:000600 ! drug tolerant
-
-[Term]
-id: OBT:002677
-name: antifungal resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002678
-name: antifungal sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002679
-name: antifungal tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002680
-name: antiviral resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002681
-name: antiviral sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002682
-name: antiviral tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002683
-name: antiyeast resistant
-is_a: OBT:002337 ! antimicrobial resistant
-
-[Term]
-id: OBT:002684
-name: antiyeast sensitive
-is_a: OBT:002338 ! antimicrobial sensitive
-
-[Term]
-id: OBT:002685
-name: antiyeast tolerant
-is_a: OBT:002339 ! antimicrobial tolerant
-
-[Term]
-id: OBT:002686
-name: aquatic plant
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:000393 ! plant
-
-[Term]
-id: OBT:002687
-name: aquifer
-is_a: OBT:002468 ! groundwater body
-
-[Term]
-id: OBT:002688
-name: bone marrow
-is_a: OBT:000334 ! lymphatic system part
-is_a: OBT:000465 ! vertebrate part
-
-[Term]
-id: OBT:002689
-name: brain
-is_a: OBT:000357 ! nervous system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002690
-name: bread wheat product
-synonym: "common wheat" EXACT [TyDI:51258]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002691
-name: brine pool
-is_a: OBT:002371 ! brackish water
-
-[Term]
-id: OBT:002692
-name: broiler meat strip
-is_a: OBT:002394 ! chicken meat
-
-[Term]
-id: OBT:002693
-name: brown dog tick
-synonym: "Rhipicephalus sanguineus" EXACT [TyDI:53820]
-is_a: OBT:002424 ! dog tick
-
-[Term]
-id: OBT:002694
-name: clinic
-synonym: "clinical center" EXACT [TyDI:52715]
-is_a: OBT:002518 ! medical center
-
-[Term]
-id: OBT:002695
-name: coal mine lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002696
-name: cold-seep sediment
-is_a: OBT:002420 ! deep-sea sediment
-
-[Term]
-id: OBT:002697
-name: community
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002698
-name: cruise ship passenger
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002699
-name: cultivated plant
-is_a: OBT:000035 ! agricultural species
-is_a: OBT:000912 ! terrestrial plant
-
-[Term]
-id: OBT:002700
-name: deer herd meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002701
-name: durum wheat product
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002702
-name: einkorn wheat product
-synonym: "einkorn" EXACT [TyDI:51248]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002703
-name: embryonic root
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002704
-name: embryonic root part
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002705
-name: emmer wheat product
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002706
-name: estuarine sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002707
-name: faucet handle
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:000330 ! kitchen equipment
-
-[Term]
-id: OBT:002708
-name: fracture water
-is_a: OBT:002467 ! ground water
-
-[Term]
-id: OBT:002709
-name: glacier
-is_a: OBT:000238 ! cold temperature environment
-is_a: OBT:000446 ! terrestrial landscape
-
-[Term]
-id: OBT:002710
-name: graft recipient
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002711
-name: halotolerant
-is_a: OBT:000370 ! osmotolerant
-is_a: OBT:000382 ! phenotype wrt habitat salinity
-
-[Term]
-id: OBT:002712
-name: healthy person
-synonym: "healthy human" RELATED [TyDI:53840]
-synonym: "healthy individual" RELATED [TyDI:53841]
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002713
-name: heart
-is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002714
-name: hospital
-synonym: "hospital environment" RELATED [TyDI:52520]
-is_a: OBT:002518 ! medical center
-
-[Term]
-id: OBT:002715
-name: hospital water distribution system
-is_a: OBT:002486 ! hospital water supply
-
-[Term]
-id: OBT:002716
-name: human body louse
-is_a: OBT:002490 ! human louse
-
-[Term]
-id: OBT:002717
-name: human head louse
-is_a: OBT:002490 ! human louse
-
-[Term]
-id: OBT:002718
-name: hydrothermal vent
-synonym: "hydrothermal vent system" RELATED [TyDI:57847]
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002719
-name: hydrothermal vent chimney
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002720
-name: hypersaline water
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:002721
-name: hypocotyl
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002722
-name: intertidal sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002723
-name: khorasan product
-synonym: "oriental wheat" RELATED [TyDI:51251]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002724
-name: kidney
-is_a: OBT:000364 ! organ
-is_a: OBT:000463 ! urogenital tract part
-
-[Term]
-id: OBT:002725
-name: liver
-is_a: OBT:000258 ! digestive system part
-is_a: OBT:000364 ! organ
-
-[Term]
-id: OBT:002726
-name: livestock
-synonym: "farm animal" RELATED [TyDI:54357]
-is_a: OBT:000035 ! agricultural species
-is_a: OBT:000596 ! domestic animal
-
-[Term]
-id: OBT:002727
-name: mouse
-synonym: "mice" EXACT [TyDI:52338]
-is_a: OBT:002530 ! murine
-
-[Term]
-id: OBT:002728
-name: muskmelon
-is_a: OBT:002519 ! melon as food
-
-[Term]
-id: OBT:002729
-name: nugget
-is_a: OBT:002394 ! chicken meat
-
-[Term]
-id: OBT:002730
-name: ocean trench
-is_a: OBT:000307 ! high pressure environment
-is_a: OBT:000338 ! marine environment
-
-[Term]
-id: OBT:002731
-name: ostrich meat
-is_a: OBT:002576 ! ratite meat
-
-[Term]
-id: OBT:002732
-name: phytopathogen
-synonym: "plant pathogen" EXACT [TyDI:58445]
-is_a: OBT:000375 ! pathogen
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:002733
-name: plant commensal
-is_a: OBT:000239 ! commensal
-is_a: OBT:000394 ! plant hosted
-
-[Term]
-id: OBT:002734
-name: plant symbiont
-synonym: "phytosymbiont" EXACT [TyDI:58446]
-is_a: OBT:000394 ! plant hosted
-is_a: OBT:000441 ! symbiont
-
-[Term]
-id: OBT:002735
-name: rainwater
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:002736
-name: rat
-is_a: OBT:002530 ! murine
-
-[Term]
-id: OBT:002737
-name: red deer meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002738
-name: roe deer meat
-is_a: OBT:002421 ! deer meat
-
-[Term]
-id: OBT:002739
-name: sake brewery
-is_a: OBT:002372 ! brewery
-
-[Term]
-id: OBT:002740
-name: salted lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002741
-name: shoot apex
-is_a: OBT:002433 ! embryonic axis part
-
-[Term]
-id: OBT:002742
-name: skin lesion
-synonym: "break in the skin" RELATED [TyDI:52525]
-is_a: OBT:000332 ! lesion
-is_a: OBT:000424 ! skin part
-
-[Term]
-id: OBT:002743
-name: small ruminant
-is_a: OBT:002589 ! ruminant
-
-[Term]
-id: OBT:002744
-name: soda lake sediment
-is_a: OBT:002499 ! lake sediment
-
-[Term]
-id: OBT:002745
-name: sourdough bread
-is_a: OBT:002503 ! leavened bread
-
-[Term]
-id: OBT:002746
-name: spelt product
-synonym: "dinkel wheat" EXACT [TyDI:51245]
-is_a: OBT:002643 ! wheat product
-
-[Term]
-id: OBT:002747
-name: stormwater
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:002748
-name: theatre shoe
-synonym: "theatre boot" EXACT [TyDI:52073]
-is_a: OBT:000341 ! medical outfit
-is_a: OBT:000420 ! shoe
-
-[Term]
-id: OBT:002749
-name: tidal flat sediment
-is_a: OBT:002402 ! coastal sediment
-
-[Term]
-id: OBT:002750
-name: vegetarian
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:002751
-name: vinegar factory
-is_a: OBT:002372 ! brewery
-
-[Term]
-id: OBT:002752
-name: waste treatment equipment
-is_a: OBT:000167 ! waste treatment environment
-is_a: OBT:000684 ! industrial equipment
-
-[Term]
-id: OBT:002753
-name: waste treatment plant
-is_a: OBT:000167 ! waste treatment environment
-is_a: OBT:000683 ! industrial building
-
-[Term]
-id: OBT:002754
-name: waste water
-synonym: "wastewater" EXACT [TyDI:58161]
-is_a: OBT:000325 ! industrial water and effluent
-is_a: OBT:000467 ! waste
-
-[Term]
-id: OBT:002755
-name: whirlpool spa
-is_a: OBT:002603 ! spa
-
-[Term]
-id: OBT:002756
-name: yeast bread
-is_a: OBT:002503 ! leavened bread
-
-[Term]
-id: OBT:002757
-name: activated carbon filter
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002758
-name: algae
-is_a: OBT:002686 ! aquatic plant
-
-[Term]
-id: OBT:002759
-name: alluvial gravel aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002760
-name: aminoglycosides resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002761
-name: amoxicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002762
-name: ampicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002763
-name: ampicillin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002764
-name: animal opportunist
-is_a: OBT:000195 ! animal hosted
-is_a: OBT:000776 ! opportunistic pathogen
-
-[Term]
-id: OBT:002765
-name: antagonist
-is_a: OBT:002732 ! phytopathogen
-
-[Term]
-id: OBT:002766
-name: biofilter
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002767
-name: black smoker
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002768
-name: black smoker chimney
-is_a: OBT:002719 ! hydrothermal vent chimney
-
-[Term]
-id: OBT:002769
-name: brine
-is_a: OBT:002691 ! brine pool
-
-[Term]
-id: OBT:002770
-name: cantaloupe as food
-synonym: "mushmelon" RELATED [TyDI:53523]
-synonym: "rockmelon" RELATED [TyDI:53524]
-synonym: "spanspek" RELATED [TyDI:53525]
-synonym: "sweet melon" RELATED [TyDI:53526]
-is_a: OBT:002728 ! muskmelon
-
-[Term]
-id: OBT:002771
-name: cereal crop
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002772
-name: chloramphenicol resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002773
-name: ciprofloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002774
-name: ciprofloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002775
-name: ciprofloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002776
-name: coastal aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002777
-name: coffee plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002778
-name: contaminated sediment
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:001303 ! sediment
-
-[Term]
-id: OBT:002779
-name: cotton plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002780
-name: cultivated Leguminosae
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002781
-name: decantation tank
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002782
-name: deep-sea hot vent
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002783
-name: deep-sea hydrothermal vent
-synonym: "deep-sea hydrothermal vent site" EXACT [TyDI:49702]
-is_a: OBT:002718 ! hydrothermal vent
-
-[Term]
-id: OBT:002784
-name: deep-sea hydrothermal vent chimney
-is_a: OBT:002719 ! hydrothermal vent chimney
-
-[Term]
-id: OBT:002785
-name: dendritic cell
-is_a: OBT:000320 ! immune cell
-is_a: OBT:000801 ! phagocyte
-
-[Term]
-id: OBT:002786
-name: digester
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002787
-name: dish towel
-is_a: OBT:000330 ! kitchen equipment
-is_a: OBT:000926 ! towel
-
-[Term]
-id: OBT:002788
-name: drilling bore water
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002789
-name: endothelium
-synonym: "endothelial" RELATED [TyDI:52445]
-synonym: "vascular endothelium" EXACT [TyDI:52444]
-is_a: OBT:000231 ! circulatory system part
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:002790
-name: erythromycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002791
-name: eschar
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:002792
-name: ethambutol resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002793
-name: fish
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:002794
-name: flooded soil
-is_a: OBT:000427 ! soil
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:002795
-name: flowing water
-synonym: "running water" RELATED [TyDI:51473]
-is_a: OBT:000269 ! environment water
-is_a: OBT:000713 ! lotic water body
-
-[Term]
-id: OBT:002796
-name: food processing wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002797
-name: gentamicin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002798
-name: gentamicin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002799
-name: geothermal aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002800
-name: ginseng plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002801
-name: glycopeptide antibiotics resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002802
-name: granitic rock aquifer
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002803
-name: grapevine
-synonym: "grapewine" EXACT [TyDI:52433]
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002804
-name: home plumbing
-synonym: "home plumbing system" EXACT [TyDI:56063]
-is_a: OBT:000260 ! domestic appliance
-is_a: OBT:000960 ! water transport structure
-
-[Term]
-id: OBT:002805
-name: hot water distribution system
-is_a: OBT:002715 ! hospital water distribution system
-
-[Term]
-id: OBT:002806
-name: human pathogen
-is_a: OBT:002669 ! animal pathogen
-
-[Term]
-id: OBT:002807
-name: industrial effluent treatment plant
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:002808
-name: industrial wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002809
-name: insect pathogen
-is_a: OBT:002669 ! animal pathogen
-
-[Term]
-id: OBT:002810
-name: intestine
-synonym: "enteric" RELATED [TyDI:53834]
-synonym: "enteroinvasive" RELATED [TyDI:53837]
-synonym: "gut" RELATED [TyDI:51589]
-synonym: "intestinal" RELATED [TyDI:53832]
-synonym: "intestinal environment" RELATED [TyDI:53835]
-synonym: "intestinal region" RELATED [TyDI:53836]
-synonym: "intestinal tract" EXACT [TyDI:53833]
-is_a: OBT:000364 ! organ
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:002811
-name: isoniazid resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002812
-name: leaching column
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002813
-name: malt vinegar brewery
-is_a: OBT:002751 ! vinegar factory
-
-[Term]
-id: OBT:002814
-name: marine microbial mat
-is_a: OBT:000338 ! marine environment
-is_a: OBT:000737 ! microbial mat
-
-[Term]
-id: OBT:002815
-name: marine wetland
-is_a: OBT:000338 ! marine environment
-is_a: OBT:000964 ! wetland
-
-[Term]
-id: OBT:002816
-name: meltwater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002817
-name: meticillin resistant
-synonym: "methicillin resistant" EXACT [TyDI:50715]
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002818
-name: meticillin sensitive
-synonym: "methicillin sensitive" EXACT [TyDI:56624]
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002819
-name: meticillin tolerant
-synonym: "methicillin tolerant" EXACT [TyDI:56655]
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002820
-name: moxifloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002821
-name: moxifloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002822
-name: moxifloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002823
-name: naladixic acid resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002824
-name: norfloxacin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002825
-name: norfloxacin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002826
-name: norfloxacin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002827
-name: obligate phytopathogen
-is_a: OBT:002732 ! phytopathogen
-
-[Term]
-id: OBT:002828
-name: oil field water
-synonym: "oil field production water" RELATED [TyDI:53128]
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002829
-name: penicillin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002830
-name: penicillin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002831
-name: penicillin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002832
-name: pharynx
-is_a: OBT:000408 ! respiratory tract part
-is_a: OBT:000642 ! gastrointestinal tract part
-
-[Term]
-id: OBT:002833
-name: plant facultative symbiont
-is_a: OBT:002734 ! plant symbiont
-
-[Term]
-id: OBT:002834
-name: plant litter
-is_a: OBT:000365 ! organic matter
-is_a: OBT:000885 ! soil matter
-
-[Term]
-id: OBT:002835
-name: plant obligate symbiont
-is_a: OBT:002734 ! plant symbiont
-
-[Term]
-id: OBT:002836
-name: plumule
-is_a: OBT:002741 ! shoot apex
-
-[Term]
-id: OBT:002837
-name: probiotic feed
-synonym: "animal probiotic" EXACT []
-is_a: OBT:000038 ! animal feed
-is_a: OBT:001269 ! probiotic food
-
-[Term]
-id: OBT:002838
-name: produced water
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002839
-name: pyrazinamide resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002840
-name: quinolone resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002841
-name: radicle
-is_a: OBT:002704 ! embryonic root part
-
-[Term]
-id: OBT:002842
-name: rennet
-is_a: OBT:000432 ! starter culture
-is_a: OBT:000477 ! additive
-
-[Term]
-id: OBT:002843
-name: resistance to amikacin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002844
-name: resistance to cotrimoxazole
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002845
-name: resistance to dalfopristin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002846
-name: resistance to imipenem
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002847
-name: resistance to levofloxacin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002848
-name: resistance to quinupristin
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002849
-name: rifampin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002850
-name: root
-synonym: "root system" RELATED [TyDI:53850]
-is_a: OBT:000411 ! rhizosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002851
-name: saline wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002852
-name: sand aquifer
-synonym: "sandy aquifer" EXACT [TyDI:53859]
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002853
-name: scald
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:002854
-name: sewage pipe
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002855
-name: sewage plant
-synonym: "sewage treatment plant" EXACT [TyDI:51613]
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:002856
-name: shower curtain
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:000580 ! curtain
-
-[Term]
-id: OBT:002857
-name: spectinomycin-resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002858
-name: streptomycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002859
-name: submersed aquatic plant
-synonym: "submerged aquatic plant" EXACT [TyDI:53827]
-is_a: OBT:002686 ! aquatic plant
-
-[Term]
-id: OBT:002860
-name: sugar cane
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002861
-name: sulfamethoxazole resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002862
-name: sulfate-rich wastewater
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:002863
-name: sulfide mound
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:000746 ! mound
-
-[Term]
-id: OBT:002864
-name: susceptibility to azithromycin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002865
-name: susceptible to dalfopristin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002866
-name: susceptible to quinupristin
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002867
-name: teicoplanin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002868
-name: teicoplanin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002869
-name: tetracycline resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002870
-name: tobacco plant
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:002871
-name: trichome
-is_a: OBT:000054 ! biofilm
-is_a: OBT:001090 ! epidermis part
-
-[Term]
-id: OBT:002872
-name: trimethoprim resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002873
-name: underground mine
-is_a: OBT:000156 ! subterrestrial habitat
-is_a: OBT:001210 ! mine
-
-[Term]
-id: OBT:002874
-name: vancomycin resistant
-is_a: OBT:002674 ! antibiotic resistant
-
-[Term]
-id: OBT:002875
-name: vancomycin sensitive
-is_a: OBT:002675 ! antibiotic sensitive
-
-[Term]
-id: OBT:002876
-name: vancomycin tolerant
-is_a: OBT:002676 ! antibiotic tolerant
-
-[Term]
-id: OBT:002877
-name: waste container
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:002878
-name: water-table aquifer
-synonym: "drinking water aquifer" RELATED [TyDI:51841]
-is_a: OBT:002687 ! aquifer
-
-[Term]
-id: OBT:002879
-name: Damselfish
-synonym: "Damselfishes" EXACT [TyDI:51336]
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002880
-name: acid mine drainage
-synonym: "AMD" EXACT [TyDI:51490]
-is_a: OBT:000176 ! acid environment
-is_a: OBT:001211 ! mine drainage
-
-[Term]
-id: OBT:002881
-name: acido resistant
-synonym: "acid resistant" EXACT [TyDI:56703]
-synonym: "acidoresistant" EXACT [TyDI:56702]
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002882
-name: acido sensitive
-synonym: "acid sensitive" EXACT [TyDI:56747]
-synonym: "acidosensitive" EXACT [TyDI:56748]
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002883
-name: acido tolerant
-synonym: "acid tolerant" EXACT [TyDI:57294]
-synonym: "acidotolerant" EXACT [TyDI:57293]
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002884
-name: activated carbon biofilter
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002885
-name: activated carbon fiber felt
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002886
-name: alkali resistant
-synonym: "alkaline resistant" EXACT [TyDI:56693]
-is_a: OBT:000152 ! stress resistant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002887
-name: alkali sensitive
-synonym: "alkaline sensitive" RELATED [TyDI:56740]
-is_a: OBT:000153 ! stress sensitive
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002888
-name: alkali tolerant
-synonym: "alkaline tolerant" RELATED [TyDI:53979]
-synonym: "alkalitolerant" EXACT [TyDI:53980]
-is_a: OBT:000154 ! stress tolerant
-is_a: OBT:001712 ! phenotype wrt chemical composition
-
-[Term]
-id: OBT:002889
-name: amphipod
-is_a: OBT:000199 ! aquatic eukaryotic species
-is_a: OBT:001059 ! crustacean
-
-[Term]
-id: OBT:002890
-name: anaerobic digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002891
-name: apron
-is_a: OBT:000330 ! kitchen equipment
-is_a: OBT:001322 ! slaugterhouse equipment
-
-[Term]
-id: OBT:002892
-name: barley plant
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002893
-name: brewery wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002894
-name: bryozoan
-is_a: OBT:000694 ! invertebrate species
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:002895
-name: chemoheterotroph
-synonym: "chemo heterotroph " EXACT [TyDI:54366]
-is_a: OBT:000555 ! chemotroph
-is_a: OBT:000665 ! heterotroph
-
-[Term]
-id: OBT:002896
-name: chemolithotroph
-synonym: "chemo lithotroph " EXACT [TyDI:56147]
-is_a: OBT:000555 ! chemotroph
-is_a: OBT:000712 ! lithotroph
-
-[Term]
-id: OBT:002897
-name: cod
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002898
-name: compost biofilter
-is_a: OBT:002766 ! biofilter
-
-[Term]
-id: OBT:002899
-name: creek water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002900
-name: drinking water treatment plant
-is_a: OBT:000597 ! drinking water facility
-is_a: OBT:000961 ! water treatment plant
-
-[Term]
-id: OBT:002901
-name: dumpster
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:002902
-name: dustbin
-synonym: "garbage can" RELATED [TyDI:52087]
-synonym: "waste bin" RELATED [TyDI:52088]
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:002903
-name: farmed fish
-synonym: "farm fish" EXACT [TyDI:51578]
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002904
-name: flower
-is_a: OBT:000494 ! anthosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002905
-name: freshwater fish
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002906
-name: fruit
-is_a: OBT:000541 ! carposphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002907
-name: gravel aquifer
-is_a: OBT:002759 ! alluvial gravel aquifer
-
-[Term]
-id: OBT:002908
-name: hagfish
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:000946 ! vertebrate
-
-[Term]
-id: OBT:002909
-name: heat exchanger
-is_a: OBT:000955 ! water cooling system
-is_a: OBT:000958 ! water heater system
-
-[Term]
-id: OBT:002910
-name: inorganically contaminated sediment
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002911
-name: kelp
-is_a: OBT:002758 ! algae
-
-[Term]
-id: OBT:002912
-name: leaf litter
-is_a: OBT:002834 ! plant litter
-
-[Term]
-id: OBT:002913
-name: lining of the small intestine
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000710 ! lining
-
-[Term]
-id: OBT:002914
-name: maize plant
-synonym: "corn plant" NARROW []
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002915
-name: marine and hypersaline microbial mat
-is_a: OBT:002814 ! marine microbial mat
-
-[Term]
-id: OBT:002916
-name: mill wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002917
-name: municipal sewage plant
-synonym: "communal sewage treatment plant" EXACT [TyDI:56678]
-is_a: OBT:002855 ! sewage plant
-
-[Term]
-id: OBT:002918
-name: nozzle
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:002919
-name: oat plant
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002920
-name: oxacillin resistant
-is_a: OBT:002829 ! penicillin resistant
-
-[Term]
-id: OBT:002921
-name: pericycle
-is_a: OBT:000816 ! plant tissue
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:002922
-name: photoautotroph
-synonym: "photo autotroph " EXACT [TyDI:54396]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002923
-name: photoheterotroph
-synonym: "photo heterotroph " EXACT [TyDI:54341]
-is_a: OBT:000665 ! heterotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002924
-name: photolithoautotroph
-synonym: "photo lithoautotroph" EXACT [TyDI:53974]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:000805 ! phototroph
-
-[Term]
-id: OBT:002925
-name: pine litter
-is_a: OBT:002834 ! plant litter
-
-[Term]
-id: OBT:002926
-name: produced water from an oil well
-is_a: OBT:002838 ! produced water
-
-[Term]
-id: OBT:002927
-name: produced water of an oil reservoir
-is_a: OBT:002838 ! produced water
-
-[Term]
-id: OBT:002928
-name: pulp-bleaching waste water
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002929
-name: radioactive sediment
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002930
-name: rice plant
-synonym: "Oryza sativa" EXACT [TyDI:51517]
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002931
-name: river water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002932
-name: root nodule
-is_a: OBT:000812 ! plant nodule
-is_a: OBT:000849 ! root part
-
-[Term]
-id: OBT:002933
-name: salmonides
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:002934
-name: seaweed
-is_a: OBT:002859 ! submersed aquatic plant
-
-[Term]
-id: OBT:002935
-name: sediment contaminated by organic pollutants
-synonym: "organically contaminated sediment" EXACT [TyDI:51598]
-is_a: OBT:002778 ! contaminated sediment
-
-[Term]
-id: OBT:002936
-name: sewage disposal plant
-is_a: OBT:002855 ! sewage plant
-
-[Term]
-id: OBT:002937
-name: shallow coastal aquifer
-is_a: OBT:002776 ! coastal aquifer
-
-[Term]
-id: OBT:002938
-name: shea cake digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002939
-name: sludge digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002940
-name: soda lake
-is_a: OBT:000187 ! alkaline environment
-is_a: OBT:001171 ! lake
-
-[Term]
-id: OBT:002941
-name: stem
-is_a: OBT:000545 ! caulosphere part
-is_a: OBT:000814 ! plant organ
-
-[Term]
-id: OBT:002942
-name: stream water
-is_a: OBT:002795 ! flowing water
-
-[Term]
-id: OBT:002943
-name: tannery wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002944
-name: textile wastewater
-is_a: OBT:002808 ! industrial wastewater
-
-[Term]
-id: OBT:002945
-name: thermal resistant
-is_a: OBT:000130 ! phenotype wrt habitat temperature
-is_a: OBT:000138 ! phenotype wrt temperature impact
-is_a: OBT:000152 ! stress resistant
-
-[Term]
-id: OBT:002946
-name: thermophilic aerobic digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002947
-name: tubeworm
-is_a: OBT:000694 ! invertebrate species
-is_a: OBT:000724 ! marine eukaryotic species
-
-[Term]
-id: OBT:002948
-name: wastewater treatment digester
-is_a: OBT:002786 ! digester
-
-[Term]
-id: OBT:002949
-name: water tap
-synonym: "faucet" RELATED [TyDI:57027]
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:002950
-name: wheat plant
-synonym: "wheat" RELATED [TyDI:51628]
-is_a: OBT:002771 ! cereal crop
-
-[Term]
-id: OBT:002951
-name: zinc- and sulfate-rich wastewater
-is_a: OBT:002862 ! sulfate-rich wastewater
-
-[Term]
-id: OBT:002952
-name: acid mine water
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:002953
-name: almond
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002954
-name: amended soil
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002955
-name: ammonia oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002956
-name: amphibian
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001374 ! warm-blooded animal
-
-[Term]
-id: OBT:002957
-name: anaerobic wastewater digester
-is_a: OBT:002948 ! wastewater treatment digester
-
-[Term]
-id: OBT:002958
-name: apple
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002959
-name: arsenic oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002960
-name: avocado
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002961
-name: banana
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002962
-name: beeswax
-is_a: OBT:000477 ! additive
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:002963
-name: berry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002964
-name: blackberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002965
-name: blueberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002966
-name: cantaloupe
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002967
-name: catfish
-is_a: OBT:002905 ! freshwater fish
-
-[Term]
-id: OBT:002968
-name: cephalopod
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001215 ! mollusc
-
-[Term]
-id: OBT:002969
-name: cherry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002970
-name: cis-dichloroethene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:002971
-name: citrus fruit
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002972
-name: coal mine lake
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:002973
-name: coconut
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002974
-name: coffee
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002975
-name: cold resistant
-synonym: "low temperature resistant" RELATED [TyDI:57099]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002976
-name: contaminated water
-synonym: "polluted water" EXACT [TyDI:51293]
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:002977
-name: cotton cultivated soil
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:002978
-name: drinking water system
-is_a: OBT:000597 ! drinking water facility
-is_a: OBT:001380 ! water system
-
-[Term]
-id: OBT:002979
-name: dye textile wastewater
-is_a: OBT:002944 ! textile wastewater
-
-[Term]
-id: OBT:002980
-name: edible oil and related product
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001267 ! pressed food
-
-[Term]
-id: OBT:002981
-name: egg
-is_a: OBT:000613 ! embryonic structure
-is_a: OBT:000986 ! animal with life stage property
-
-[Term]
-id: OBT:002982
-name: extreme cold resistant
-synonym: "extreme low temperature resistant" RELATED [TyDI:57106]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002983
-name: extreme heat resistant
-synonym: "extreme high temperature resistant" RELATED [TyDI:57032]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002984
-name: ferrous iron oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002985
-name: freeze-thaw resistant
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002986
-name: grape
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002987
-name: heat resistant
-synonym: "high temperature resistant" RELATED [TyDI:57091]
-is_a: OBT:002945 ! thermal resistant
-
-[Term]
-id: OBT:002988
-name: high-level radioactive sediment
-is_a: OBT:002929 ! radioactive sediment
-
-[Term]
-id: OBT:002989
-name: hospital drinking water
-synonym: "hospital potable water" RELATED [TyDI:50807]
-is_a: OBT:000312 ! hospital water
-is_a: OBT:001530 ! drinking water
-
-[Term]
-id: OBT:002990
-name: hotspring
-synonym: "hot spring" EXACT [TyDI:49581]
-is_a: OBT:000625 ! extreme high temperature environment
-is_a: OBT:001333 ! spring
-is_a: OBT:002019 ! environmental water with physical property
-
-[Term]
-id: OBT:002991
-name: hydrogen oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:002992
-name: intestinal epithelium
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:001091 ! epithelium
-
-[Term]
-id: OBT:002993
-name: intestinal mucosa
-synonym: "gut mucosa" EXACT [TyDI:51153]
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:002994
-name: kiwi
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002995
-name: macrophage
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:002996
-name: mango
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:002997
-name: marine sponge
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001332 ! sponge
-
-[Term]
-id: OBT:002998
-name: mast cell
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:002999
-name: melon
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003000
-name: moldy peanut
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003001
-name: monocyte
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:000978 ! agranulocyte
-
-[Term]
-id: OBT:003002
-name: municipal sewage sludge digester
-is_a: OBT:002939 ! sludge digester
-
-[Term]
-id: OBT:003003
-name: naphthalene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003004
-name: neutrophil
-is_a: OBT:000801 ! phagocyte
-is_a: OBT:001134 ! granulocyte
-
-[Term]
-id: OBT:003005
-name: nitrobenzene contaminated sediment
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003006
-name: oil contaminated sediment
-synonym: "petroleum contaminated sediment" EXACT [TyDI:51375]
-is_a: OBT:002935 ! sediment contaminated by organic pollutants
-
-[Term]
-id: OBT:003007
-name: oil mill wastewater
-is_a: OBT:002916 ! mill wastewater
-
-[Term]
-id: OBT:003008
-name: olive
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003009
-name: orange
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003010
-name: papaya
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003011
-name: peach
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003012
-name: pear
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003013
-name: plant based drink
-synonym: "plant based beverage" RELATED [TyDI:53339]
-is_a: OBT:000815 ! plant product and primary derivative thereof
-is_a: OBT:001078 ! drink
-
-[Term]
-id: OBT:003014
-name: pleural empyema
-is_a: OBT:000818 ! pleural fluid
-is_a: OBT:001087 ! empyema
-
-[Term]
-id: OBT:003015
-name: plum
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003016
-name: propolis
-is_a: OBT:000477 ! additive
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003017
-name: pyritic acid mine drainage
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:003018
-name: raspberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003019
-name: rhizoplane
-synonym: "root epidermis" EXACT [TyDI:51430]
-is_a: OBT:000849 ! root part
-is_a: OBT:001089 ! epidermis
-
-[Term]
-id: OBT:003020
-name: root cortex
-is_a: OBT:000849 ! root part
-is_a: OBT:001050 ! cortex
-
-[Term]
-id: OBT:003021
-name: salmon
-is_a: OBT:002933 ! salmonides
-
-[Term]
-id: OBT:003022
-name: sauce
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001044 ! condiment
-
-[Term]
-id: OBT:003023
-name: sour anaerobic digester
-is_a: OBT:002890 ! anaerobic digester
-
-[Term]
-id: OBT:003024
-name: stem nodule
-is_a: OBT:000812 ! plant nodule
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003025
-name: strawberry
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003026
-name: submarine hydrocarbon seep
-is_a: OBT:000338 ! marine environment
-is_a: OBT:001673 ! oil seep
-
-[Term]
-id: OBT:003027
-name: sulfide-saturated mud sediment
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:001655 ! mud sediment
-
-[Term]
-id: OBT:003028
-name: sulfur oxidizing
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003029
-name: tidal marsh
-is_a: OBT:000690 ! intertidal zone
-is_a: OBT:001041 ! coastal wetland
-
-[Term]
-id: OBT:003030
-name: tomato
-is_a: OBT:002906 ! fruit
-
-[Term]
-id: OBT:003031
-name: trout
-is_a: OBT:002903 ! farmed fish
-
-[Term]
-id: OBT:003032
-name: unamended soil
-synonym: "unamended control soil" RELATED [TyDI:51282]
-is_a: OBT:000067 ! cultivated habitat
-is_a: OBT:001857 ! agricultural soil
-
-[Term]
-id: OBT:003033
-name: water pipe
-is_a: OBT:000960 ! water transport structure
-is_a: OBT:001256 ! piping system
-
-[Term]
-id: OBT:003034
-name: acid hot spring
-synonym: "acidic hot spring" EXACT [TyDI:57379]
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003035
-name: alkaline hotspring
-synonym: "alkaline hot spring" EXACT [TyDI:54989]
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003036
-name: anammox
-is_a: OBT:002955 ! ammonia oxidizing
-
-[Term]
-id: OBT:003037
-name: anoxic water
-is_a: OBT:000197 ! anoxic environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:003038
-name: arsenite oxidizing
-is_a: OBT:002959 ! arsenic oxidizing
-
-[Term]
-id: OBT:003039
-name: bedside carafe
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003040
-name: bee pollen
-is_a: OBT:001070 ! dietary supplement
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003041
-name: boar
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003042
-name: contaminated groundwater
-is_a: OBT:002976 ! contaminated water
-
-[Term]
-id: OBT:003043
-name: contaminated soil
-synonym: "polluted soil" RELATED [TyDI:53875]
-is_a: OBT:000244 ! contaminated site
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:003044
-name: decaying plant material
-synonym: "decaying plant" RELATED [TyDI:51918]
-synonym: "decaying plant tissue" RELATED [TyDI:51917]
-is_a: OBT:001065 ! decaying matter
-is_a: OBT:001258 ! plant material
-
-[Term]
-id: OBT:003045
-name: dolphin
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003046
-name: fermented liquid
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003047
-name: fermented plant-based food
-is_a: OBT:000815 ! plant product and primary derivative thereof
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003048
-name: fox
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003049
-name: fresh meat
-is_a: OBT:001200 ! meat and meat product
-is_a: OBT:001275 ! raw meat
-
-[Term]
-id: OBT:003050
-name: freshwater hotspring
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003051
-name: freshwater marsh
-is_a: OBT:001121 ! freshwater wetland
-is_a: OBT:001198 ! marsh
-
-[Term]
-id: OBT:003052
-name: frog
-is_a: OBT:002956 ! amphibian
-
-[Term]
-id: OBT:003053
-name: goulash
-is_a: OBT:001328 ! soup
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:003054
-name: grain based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003055
-name: gum tissue
-synonym: "gingiva" EXACT [TyDI:50904]
-synonym: "gingival" RELATED [TyDI:50905]
-is_a: OBT:001217 ! mouth part
-is_a: OBT:001218 ! mucosal tissue
-
-[Term]
-id: OBT:003056
-name: hare
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003057
-name: iguana
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003058
-name: juice
-is_a: OBT:001078 ! drink
-is_a: OBT:001267 ! pressed food
-
-[Term]
-id: OBT:003059
-name: leaf based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003060
-name: leaf epidermis
-is_a: OBT:001089 ! epidermis
-is_a: OBT:001175 ! leaf part
-
-[Term]
-id: OBT:003061
-name: legume based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003062
-name: lion
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003063
-name: neutral hotspring
-is_a: OBT:002990 ! hotspring
-
-[Term]
-id: OBT:003064
-name: nut based drink
-is_a: OBT:003013 ! plant based drink
-
-[Term]
-id: OBT:003065
-name: palm oil
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003066
-name: partridge
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003067
-name: petite positive
-synonym: "petite colony" EXACT [TyDI:50082]
-synonym: "petite mutant" EXACT [TyDI:50084]
-synonym: "petite strain" EXACT [TyDI:50083]
-synonym: "petite yeast" EXACT [TyDI:50081]
-is_a: OBT:000118 ! mutant
-is_a: OBT:000379 ! phenotype wrt carbon source
-is_a: OBT:000386 ! phenotype wrt shape
-
-[Term]
-id: OBT:003068
-name: pheasant
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003069
-name: pozole
-is_a: OBT:001328 ! soup
-is_a: OBT:001337 ! stew
-
-[Term]
-id: OBT:003070
-name: root endodermis
-is_a: OBT:001088 ! endodermis
-is_a: OBT:001287 ! root cortex part
-
-[Term]
-id: OBT:003071
-name: royal jelly
-is_a: OBT:001070 ! dietary supplement
-is_a: OBT:001146 ! honey and apiculture product
-
-[Term]
-id: OBT:003072
-name: saline marsh
-synonym: "salt marsh" EXACT [TyDI:50995]
-is_a: OBT:001198 ! marsh
-is_a: OBT:001290 ! saline wetland
-
-[Term]
-id: OBT:003073
-name: seal
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003074
-name: squid
-is_a: OBT:002968 ! cephalopod
-
-[Term]
-id: OBT:003075
-name: stem cortex
-is_a: OBT:001050 ! cortex
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003076
-name: stem epidermis
-is_a: OBT:001089 ! epidermis
-is_a: OBT:001336 ! stem part
-
-[Term]
-id: OBT:003077
-name: sulfide-rich water
-is_a: OBT:000437 ! sulfide-rich environment
-is_a: OBT:002018 ! environmental water with chemical property
-
-[Term]
-id: OBT:003078
-name: sunflower oil
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003079
-name: toad
-is_a: OBT:002956 ! amphibian
-
-[Term]
-id: OBT:003080
-name: Ntoba Mbodi
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003081
-name: anoxic zone of freshwater lake
-is_a: OBT:003037 ! anoxic water
-
-[Term]
-id: OBT:003082
-name: baking yeast
-synonym: "baker yeast" EXACT [TyDI:52032]
-synonym: "baker's yeast" EXACT [TyDI:52033]
-synonym: "bakery yeast" EXACT [TyDI:52031]
-is_a: OBT:000432 ! starter culture
-is_a: OBT:002657 ! yeast
-
-[Term]
-id: OBT:003083
-name: bobtail squid
-is_a: OBT:003074 ! squid
-
-[Term]
-id: OBT:003084
-name: cake
-is_a: OBT:001045 ! confectionery
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:003085
-name: carpaccio
-is_a: OBT:001275 ! raw meat
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:003086
-name: cat
-is_a: OBT:001254 ! pet
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003087
-name: cereal based drink
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003088
-name: clam juice
-is_a: OBT:003058 ! juice
-
-[Term]
-id: OBT:003089
-name: decaying fruit
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003090
-name: decaying leaf
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003091
-name: decaying wood
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003092
-name: dog
-is_a: OBT:001254 ! pet
-is_a: OBT:001625 ! mammalian
-
-[Term]
-id: OBT:003093
-name: fermented dairy product
-synonym: "fermented milk product" EXACT [TyDI:51941]
-is_a: OBT:001208 ! milk and milk product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003094
-name: fermented meat
-is_a: OBT:001200 ! meat and meat product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003095
-name: fermented seafood
-is_a: OBT:001301 ! seafood and seafood product
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003096
-name: fermented vegetable product
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003097
-name: garden lettuce
-synonym: "cultivated lettuce" EXACT [TyDI:52008]
-synonym: "Lactuca sativa" EXACT [TyDI:52007]
-is_a: OBT:000972 ! Asteraceae
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003098
-name: gingival margin
-is_a: OBT:003055 ! gum tissue
-
-[Term]
-id: OBT:003099
-name: humus-rich acidic ash soil
-is_a: OBT:000679 ! humus
-is_a: OBT:002257 ! soil with chemical property
-
-[Term]
-id: OBT:003100
-name: ice cream
-is_a: OBT:001208 ! milk and milk product
-is_a: OBT:001564 ! frozen food
-
-[Term]
-id: OBT:003101
-name: illuminated anoxic zone of aquatic environment
-is_a: OBT:000197 ! anoxic environment
-is_a: OBT:002553 ! photic zone
-
-[Term]
-id: OBT:003102
-name: kebab
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001634 ! meat based dish
-
-[Term]
-id: OBT:003103
-name: liver paste
-is_a: OBT:001199 ! mashed food
-is_a: OBT:001415 ! animal liver and product thereof
-
-[Term]
-id: OBT:003104
-name: livestock manure
-is_a: OBT:000985 ! animal waste
-is_a: OBT:001627 ! manure
-
-[Term]
-id: OBT:003105
-name: marine water
-synonym: "ocean water" EXACT [TyDI:50869]
-synonym: "sea water" EXACT [TyDI:50870]
-synonym: "seawater" EXACT [TyDI:50868]
-is_a: OBT:000338 ! marine environment
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:003106
-name: mixed salad
-synonym: "ready-to-eat salad" RELATED [TyDI:51412]
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:003107
-name: monkey
-is_a: OBT:000967 ! wild animal
-is_a: OBT:002201 ! primate
-
-[Term]
-id: OBT:003108
-name: oleaginous seed based drink
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003109
-name: olive and primary derivative thereof
-is_a: OBT:001238 ! oilfruit and primary derivative thereof
-is_a: OBT:001568 ! fruit with edible peel and primary derivative thereof
-
-[Term]
-id: OBT:003110
-name: otter
-is_a: OBT:000967 ! wild animal
-is_a: OBT:002148 ! mustelidae
-
-[Term]
-id: OBT:003111
-name: peat
-is_a: OBT:003044 ! decaying plant material
-
-[Term]
-id: OBT:003112
-name: pet bird
-is_a: OBT:001254 ! pet
-is_a: OBT:001446 ! bird
-
-[Term]
-id: OBT:003113
-name: pet turtle
-is_a: OBT:001254 ! pet
-is_a: OBT:001832 ! turtle
-
-[Term]
-id: OBT:003114
-name: pizza
-is_a: OBT:001278 ! ready-to-eat meal
-is_a: OBT:001436 ! bakery product
-
-[Term]
-id: OBT:003115
-name: salt contaminated soil
-synonym: "salty soil" RELATED [TyDI:51263]
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003116
-name: septic tank
-is_a: OBT:000098 ! household good
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:003117
-name: soil contaminated with agricultural activity
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003118
-name: soil contaminated with industrial xenobiotic compound
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003119
-name: stem endodermis
-is_a: OBT:001088 ! endodermis
-is_a: OBT:001788 ! stem cortex part
-
-[Term]
-id: OBT:003120
-name: urban soil
-is_a: OBT:003043 ! contaminated soil
-
-[Term]
-id: OBT:003121
-name: wort
-is_a: OBT:003046 ! fermented liquid
-
-[Term]
-id: OBT:003122
-name: yoghurt from bambara groundnut
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003123
-name: Euprymna scolopes
-is_a: OBT:003083 ! bobtail squid
-
-[Term]
-id: OBT:003124
-name: Gundruk
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003125
-name: animal symbiont
-is_a: OBT:000441 ! symbiont
-is_a: OBT:002668 ! animal commensal
-
-[Term]
-id: OBT:003126
-name: arsenic contaminated-soil
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003127
-name: beer wort
-is_a: OBT:003121 ! wort
-
-[Term]
-id: OBT:003128
-name: canned olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003129
-name: cattle waste
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003130
-name: chicken manure
-synonym: "chicken waste" RELATED [TyDI:51897]
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003131
-name: choux pastry
-is_a: OBT:001045 ! confectionery
-is_a: OBT:002174 ! pastry product
-
-[Term]
-id: OBT:003132
-name: coastal water
-synonym: "coastal" RELATED [TyDI:52037]
-synonym: "coastal seawater" EXACT [TyDI:52036]
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003133
-name: coral reef water
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003134
-name: cupcake
-is_a: OBT:003084 ! cake
-
-[Term]
-id: OBT:003135
-name: custard cake
-is_a: OBT:003084 ! cake
-
-[Term]
-id: OBT:003136
-name: decaying apple
-is_a: OBT:003089 ! decaying fruit
-
-[Term]
-id: OBT:003137
-name: decaying bamboo leaf
-is_a: OBT:003090 ! decaying leaf
-
-[Term]
-id: OBT:003138
-name: decaying bark
-is_a: OBT:003091 ! decaying wood
-
-[Term]
-id: OBT:003139
-name: donkey
-is_a: OBT:001384 ! working animal
-is_a: OBT:002078 ! herbivore
-
-[Term]
-id: OBT:003140
-name: emesis basin
-synonym: "kidney dish" RELATED [TyDI:52084]
-is_a: OBT:000108 ! medical equipment
-is_a: OBT:002877 ! waste container
-
-[Term]
-id: OBT:003141
-name: farmyard manure
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003142
-name: fermented beet
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003143
-name: fermented butter
-synonym: "beurre" EXACT [TyDI:53955]
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003144
-name: fermented cereal-based product
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-is_a: OBT:001546 ! fermented food
-
-[Term]
-id: OBT:003145
-name: fermented fish product
-is_a: OBT:001546 ! fermented food
-is_a: OBT:001549 ! fish meat and fish meat product
-
-[Term]
-id: OBT:003146
-name: fermented milk
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003147
-name: fermented shrimp paste
-is_a: OBT:003095 ! fermented seafood
-
-[Term]
-id: OBT:003148
-name: fertilized soil
-is_a: OBT:003117 ! soil contaminated with agricultural activity
-
-[Term]
-id: OBT:003149
-name: fish roe and product thereof
-is_a: OBT:001301 ! seafood and seafood product
-is_a: OBT:001872 ! animal roe
-
-[Term]
-id: OBT:003150
-name: fish waste
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003151
-name: garlic plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003152
-name: gelato
-is_a: OBT:003100 ! ice cream
-
-[Term]
-id: OBT:003153
-name: granita
-is_a: OBT:001564 ! frozen food
-is_a: OBT:001842 ! water based dish
-
-[Term]
-id: OBT:003154
-name: horse manure
-synonym: "horse waste" RELATED [TyDI:51713]
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003155
-name: hospital humidifier
-is_a: OBT:001153 ! humidifier
-is_a: OBT:002082 ! hospital equipment
-
-[Term]
-id: OBT:003156
-name: ill person
-is_a: OBT:000491 ! animal with disease
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003157
-name: metal contaminated soil
-synonym: "metal-stressed soil" RELATED [TyDI:52335]
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003158
-name: olive as food
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003159
-name: onion plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-
-[Term]
-id: OBT:003160
-name: pesticide enriched soil
-is_a: OBT:003117 ! soil contaminated with agricultural activity
-
-[Term]
-id: OBT:003161
-name: pig manure
-is_a: OBT:003104 ! livestock manure
-
-[Term]
-id: OBT:003162
-name: roadside soil
-is_a: OBT:003120 ! urban soil
-
-[Term]
-id: OBT:003163
-name: salt stressed soil
-is_a: OBT:003115 ! salt contaminated soil
-
-[Term]
-id: OBT:003164
-name: saltern
-is_a: OBT:000050 ! artificial water environment
-is_a: OBT:000667 ! high salt concentration environment
-is_a: OBT:000705 ! lentic water body
-
-[Term]
-id: OBT:003165
-name: sauerkraut
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003166
-name: sorbet
-is_a: OBT:001564 ! frozen food
-is_a: OBT:001565 ! fruit based dish
-
-[Term]
-id: OBT:003167
-name: stratified marine water column
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003168
-name: submarine
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003169
-name: submarinegroundwater discharge
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003170
-name: sugar-beet refinery
-is_a: OBT:001281 ! refinery
-is_a: OBT:002275 ! sugar factory
-
-[Term]
-id: OBT:003171
-name: sushi
-is_a: OBT:001548 ! fish based dish
-is_a: OBT:001744 ! rice based dish
-
-[Term]
-id: OBT:003172
-name: table olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003173
-name: tsetse fly
-synonym: "tsetse" EXACT [TyDI:52216]
-synonym: "tsetse host" RELATED [TyDI:52215]
-is_a: OBT:001453 ! blood-feeding insect
-is_a: OBT:001553 ! fly
-
-[Term]
-id: OBT:003174
-name: wastewater treatment equipment
-is_a: OBT:000201 ! artificial water structure
-is_a: OBT:002752 ! waste treatment equipment
-
-[Term]
-id: OBT:003175
-name: young adult
-is_a: OBT:001395 ! adult animal
-is_a: OBT:001849 ! young animal
-
-[Term]
-id: OBT:003176
-name: Cu-stressed soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003177
-name: Glossina
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003178
-name: acidified beer wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003179
-name: adolescent
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003180
-name: adult tsetse fly
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003181
-name: amasi
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003182
-name: animal facultative symbiont
-is_a: OBT:003125 ! animal symbiont
-
-[Term]
-id: OBT:003183
-name: animal obligate symbiont
-is_a: OBT:003125 ! animal symbiont
-
-[Term]
-id: OBT:003184
-name: baby
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003185
-name: cheesecake
-is_a: OBT:003135 ! custard cake
-
-[Term]
-id: OBT:003186
-name: chicken faeces
-is_a: OBT:003130 ! chicken manure
-
-[Term]
-id: OBT:003187
-name: chicken yard waste
-is_a: OBT:003130 ! chicken manure
-
-[Term]
-id: OBT:003188
-name: child
-synonym: "children" EXACT [TyDI:52112]
-is_a: OBT:000986 ! animal with life stage property
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003189
-name: chromate contaminated soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003190
-name: cinnamon
-synonym: " Cinnamomum aromaticum" EXACT [TyDI:54701]
-is_a: OBT:001784 ! spice
-is_a: OBT:001954 ! cinnamon and related product
-
-[Term]
-id: OBT:003191
-name: cod roe
-synonym: "cod egg" RELATED [TyDI:53412]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003192
-name: constructed wetland
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003193
-name: dadih
-synonym: "dadiah" EXACT [TyDI:53365]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003194
-name: dahi
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003195
-name: dry sausage
-is_a: OBT:001758 ! sausage
-is_a: OBT:002002 ! dried animal product
-
-[Term]
-id: OBT:003196
-name: female tsetse fly
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003197
-name: filmjölk
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003198
-name: fjord water
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003199
-name: flatfish-Sikhae
-is_a: OBT:003145 ! fermented fish product
-
-[Term]
-id: OBT:003200
-name: freshwater lake
-is_a: OBT:001171 ! lake
-is_a: OBT:002455 ! freshwater
-
-[Term]
-id: OBT:003201
-name: ginger
-is_a: OBT:001784 ! spice
-is_a: OBT:002061 ! ginger and related product
-
-[Term]
-id: OBT:003202
-name: glassy rim of the pillow basalt
-is_a: OBT:001583 ! glassy rind of lava
-is_a: OBT:002274 ! submarine glassy basalt
-
-[Term]
-id: OBT:003203
-name: heavy metal contaminated soil
-is_a: OBT:003157 ! metal contaminated soil
-
-[Term]
-id: OBT:003204
-name: herbicide enriched soil
-is_a: OBT:003160 ! pesticide enriched soil
-
-[Term]
-id: OBT:003205
-name: hopped wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003206
-name: immunodeficient person
-synonym: "compromised host" EXACT [TyDI:52133]
-synonym: "compromised patient" EXACT [TyDI:52131]
-synonym: "immune-compromised patient" EXACT [TyDI:52134]
-synonym: "immune-compromised person" EXACT [TyDI:52132]
-synonym: "immunocompromised host" EXACT [TyDI:52137]
-synonym: "immunodeppressed subject" EXACT [TyDI:52136]
-synonym: "immunodepressed person" EXACT [TyDI:52135]
-is_a: OBT:003156 ! ill person
-
-[Term]
-id: OBT:003207
-name: insecticide enriched soil
-is_a: OBT:003160 ! pesticide enriched soil
-
-[Term]
-id: OBT:003208
-name: kazunoko
-synonym: "herring egg" RELATED [TyDI:53407]
-synonym: "herring roe" RELATED [TyDI:53406]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003209
-name: kefir
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003210
-name: kumis
-synonym: "koumiss" EXACT [TyDI:53355]
-synonym: "kumiss" EXACT [TyDI:53356]
-synonym: "kumys" EXACT [TyDI:53354]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003211
-name: laboratory mice
-is_a: OBT:000700 ! laboratory animal
-is_a: OBT:002727 ! mouse
-
-[Term]
-id: OBT:003212
-name: laboratory rat
-is_a: OBT:000700 ! laboratory animal
-is_a: OBT:002736 ! rat
-
-[Term]
-id: OBT:003213
-name: lagoon
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003214
-name: långfil
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003215
-name: malt
-synonym: "malted barley" EXACT [TyDI:51069]
-is_a: OBT:001479 ! cereal grain and primary derivative thereof
-is_a: OBT:002007 ! dried plant product
-
-[Term]
-id: OBT:003216
-name: masago
-synonym: "smelt egg" RELATED [TyDI:53399]
-synonym: "smelt roe" RELATED [TyDI:53398]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003217
-name: matsoni
-synonym: " Caspian Sea yoghurt" EXACT [TyDI:53361]
-synonym: "matzoon" EXACT [TyDI:53362]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003218
-name: munkoyo
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003219
-name: pantothenate enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003220
-name: patient
-synonym: "person with treated disease" RELATED [TyDI:52061]
-synonym: "treated patient" EXACT [TyDI:52062]
-is_a: OBT:003156 ! ill person
-
-[Term]
-id: OBT:003221
-name: peritrophic membrane
-is_a: OBT:000200 ! arthropod part
-is_a: OBT:000642 ! gastrointestinal tract part
-is_a: OBT:000730 ! animal membrane
-
-[Term]
-id: OBT:003222
-name: pet rabbit
-is_a: OBT:001254 ! pet
-is_a: OBT:002572 ! rabbit
-
-[Term]
-id: OBT:003223
-name: plum as food
-synonym: "plum" EXACT [TyDI:50276]
-is_a: OBT:001796 ! stone fruit and primary derivative thereof
-is_a: OBT:002191 ! plum and primary derivative thereof
-
-[Term]
-id: OBT:003224
-name: puparia
-is_a: OBT:003173 ! tsetse fly
-
-[Term]
-id: OBT:003225
-name: salicylate enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003226
-name: saline lake
-is_a: OBT:001171 ! lake
-is_a: OBT:002592 ! saline water
-
-[Term]
-id: OBT:003227
-name: saltern crystallizer pond
-is_a: OBT:003164 ! saltern
-
-[Term]
-id: OBT:003228
-name: sandwich bread
-synonym: "pan bread" RELATED [TyDI:55070]
-is_a: OBT:001436 ! bakery product
-is_a: OBT:001913 ! bread
-
-[Term]
-id: OBT:003229
-name: shower head
-is_a: OBT:000208 ! bathroom equipment
-is_a: OBT:002804 ! home plumbing
-
-[Term]
-id: OBT:003230
-name: skin abscess
-is_a: OBT:000476 ! abscess
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:003231
-name: skin wound
-is_a: OBT:000970 ! wound
-is_a: OBT:002742 ! skin lesion
-
-[Term]
-id: OBT:003232
-name: soil of roadside tree
-is_a: OBT:003162 ! roadside soil
-
-[Term]
-id: OBT:003233
-name: solar saltern
-is_a: OBT:003164 ! saltern
-
-[Term]
-id: OBT:003234
-name: sour milk
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003235
-name: tobiko
-synonym: "flying fish egg" RELATED [TyDI:53417]
-synonym: "flying fish roe" RELATED [TyDI:53418]
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003236
-name: unhopped wort
-is_a: OBT:003127 ! beer wort
-
-[Term]
-id: OBT:003237
-name: urea enriched soil
-is_a: OBT:003148 ! fertilized soil
-
-[Term]
-id: OBT:003238
-name: viili
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003239
-name: wastewater treatment plant
-synonym: "waste water treatment plant" EXACT [TyDI:50814]
-is_a: OBT:000961 ! water treatment plant
-is_a: OBT:002753 ! waste treatment plant
-
-[Term]
-id: OBT:003240
-name: xueo
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003241
-name: yogurt
-synonym: "yoghourt" EXACT [TyDI:51972]
-synonym: "yoghurt" EXACT [TyDI:51971]
-is_a: OBT:003146 ! fermented milk
-
-[Term]
-id: OBT:003242
-name: éclair
-is_a: OBT:003135 ! custard cake
-
-[Term]
-id: OBT:003243
-name: Bulgarian yogurt
-is_a: OBT:003241 ! yogurt
-
-[Term]
-id: OBT:003244
-name: Morcela de Arroz
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003245
-name: adult human
-is_a: OBT:001395 ! adult animal
-is_a: OBT:002488 ! human
-
-[Term]
-id: OBT:003246
-name: agricultural wastewater treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003247
-name: bite
-is_a: OBT:003231 ! skin wound
-
-[Term]
-id: OBT:003248
-name: boy
-is_a: OBT:003188 ! child
-
-[Term]
-id: OBT:003249
-name: brown mushroom
-synonym: "baby bella" EXACT [TyDI:54258]
-synonym: "brown cap mushroom" EXACT [TyDI:54259]
-synonym: "chestnut mushroom" EXACT [TyDI:54254]
-synonym: "cremini" EXACT [TyDI:54255]
-synonym: "crimini mushroom" EXACT [TyDI:54253]
-synonym: "Italian brown" EXACT [TyDI:54261]
-synonym: "Italian mushroom" EXACT [TyDI:54256]
-synonym: "Roman brown mushroom" EXACT [TyDI:54260]
-synonym: "Swiss brown mushroom" EXACT [TyDI:54257]
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003250
-name: cep
-is_a: OBT:001941 ! cep and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003251
-name: cheese factory
-is_a: OBT:001988 ! dairy processing plant
-is_a: OBT:002039 ! food fermentation factory
-
-[Term]
-id: OBT:003252
-name: chloropicrine-enriched soil
-is_a: OBT:003204 ! herbicide enriched soil
-
-[Term]
-id: OBT:003253
-name: chorizo
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003254
-name: common mushroom
-synonym: "button mushroom" EXACT [TyDI:54266]
-synonym: "champignon mushroom" EXACT [TyDI:54264]
-synonym: "cultivated mushroom" EXACT [TyDI:54267]
-synonym: "table mushroom" EXACT [TyDI:54265]
-synonym: "white mushroom" EXACT [TyDI:54268]
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003255
-name: cultivated crucifer
-is_a: OBT:001057 ! crucifer
-is_a: OBT:002699 ! cultivated plant
-
-[Term]
-id: OBT:003256
-name: digestive chamber
-is_a: OBT:000641 ! gastrointestinal tract
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003257
-name: domestic wastewater treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003258
-name: furuncle
-synonym: "boil" RELATED [TyDI:52122]
-is_a: OBT:003230 ! skin abscess
-
-[Term]
-id: OBT:003259
-name: girl
-is_a: OBT:003188 ! child
-
-[Term]
-id: OBT:003260
-name: highly alkaline saline soda lake
-is_a: OBT:003226 ! saline lake
-
-[Term]
-id: OBT:003261
-name: hypersaline lake
-is_a: OBT:003226 ! saline lake
-
-[Term]
-id: OBT:003262
-name: industrial waste water treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003263
-name: infant
-is_a: OBT:003184 ! baby
-
-[Term]
-id: OBT:003264
-name: marine fish
-is_a: OBT:000724 ! marine eukaryotic species
-is_a: OBT:002793 ! fish
-
-[Term]
-id: OBT:003265
-name: mercury-enriched soil
-is_a: OBT:003203 ! heavy metal contaminated soil
-
-[Term]
-id: OBT:003266
-name: mine waste water
-synonym: "mine wastewater" EXACT [TyDI:51583]
-synonym: "mine water" EXACT []
-is_a: OBT:001212 ! mine waste
-is_a: OBT:002754 ! waste water
-
-[Term]
-id: OBT:003267
-name: morel
-is_a: OBT:002055 ! fungi as food
-is_a: OBT:002141 ! morel and related product
-
-[Term]
-id: OBT:003268
-name: open skin wound
-is_a: OBT:003231 ! skin wound
-
-[Term]
-id: OBT:003269
-name: patient with infectious disease
-is_a: OBT:003220 ! patient
-
-[Term]
-id: OBT:003270
-name: portobello mushroom
-is_a: OBT:001968 ! common mushroom and related product
-is_a: OBT:002055 ! fungi as food
-
-[Term]
-id: OBT:003271
-name: rainwater treatment utility
-synonym: "stormwater treatment utility" EXACT [TyDI:56468]
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003272
-name: root hair
-is_a: OBT:000849 ! root part
-is_a: OBT:002871 ! trichome
-
-[Term]
-id: OBT:003273
-name: sea urchin roe
-is_a: OBT:001872 ! animal roe
-is_a: OBT:002299 ! urchin and product thereof
-
-[Term]
-id: OBT:003274
-name: submarine thermal spring
-is_a: OBT:000318 ! hydrotelluric environment
-is_a: OBT:000338 ! marine environment
-is_a: OBT:001820 ! thermal spring
-
-[Term]
-id: OBT:003275
-name: truffle
-is_a: OBT:002055 ! fungi as food
-is_a: OBT:002296 ! truffle and related product
-
-[Term]
-id: OBT:003276
-name: water pollution treatment plant
-is_a: OBT:003239 ! wastewater treatment plant
-
-[Term]
-id: OBT:003277
-name: Medicago
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003278
-name: brocoli
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003279
-name: brussel sprout
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003280
-name: cabbage
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003281
-name: chemo litho autotroph
-synonym: "lithoautotroph " EXACT [TyDI:54352]
-is_a: OBT:000499 ! autotroph
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003282
-name: chemoorganoheterotroph
-synonym: "chemo hetero organotroph" EXACT [TyDI:56150]
-synonym: "chemo organo heterotroph " EXACT [TyDI:56151]
-is_a: OBT:000778 ! organotroph
-is_a: OBT:002895 ! chemoheterotroph
-
-[Term]
-id: OBT:003283
-name: dairy wastewater treatment plant
-is_a: OBT:003246 ! agricultural wastewater treatment plant
-
-[Term]
-id: OBT:003284
-name: diner
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003285
-name: elderly person
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003286
-name: extreme acid mine drainage
-is_a: OBT:000626 ! extremely acid environment
-is_a: OBT:002880 ! acid mine drainage
-
-[Term]
-id: OBT:003287
-name: fenugreek
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003288
-name: formula fed infant
-is_a: OBT:003263 ! infant
-
-[Term]
-id: OBT:003289
-name: gold mine wastewater
-is_a: OBT:003266 ! mine waste water
-
-[Term]
-id: OBT:003290
-name: guar plant
-synonym: "Cyamopsis Tetragonaloba" EXACT [TyDI:52176]
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003291
-name: inmate
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003292
-name: large intestine
-is_a: OBT:001184 ! lower gastrointestinal tract part
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003293
-name: low temperature ground water
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:002467 ! ground water
-
-[Term]
-id: OBT:003294
-name: mackerel
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003295
-name: mammalian livestock
-is_a: OBT:001625 ! mammalian
-is_a: OBT:002726 ! livestock
-
-[Term]
-id: OBT:003296
-name: mung bean plant
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003297
-name: nursing home resident
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003298
-name: pea plant
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003299
-name: photoorganoheterotroph
-synonym: "photo organoheterotroph" EXACT [TyDI:56968]
-is_a: OBT:000778 ! organotroph
-is_a: OBT:002923 ! photoheterotroph
-
-[Term]
-id: OBT:003300
-name: poultry
-is_a: OBT:001446 ! bird
-is_a: OBT:002726 ! livestock
-
-[Term]
-id: OBT:003301
-name: ripening room
-is_a: OBT:003251 ! cheese factory
-
-[Term]
-id: OBT:003302
-name: sardine
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003303
-name: small intestine
-is_a: OBT:001366 ! upper gastrointestinal tract part
-is_a: OBT:002810 ! intestine
-
-[Term]
-id: OBT:003304
-name: soybean plant
-synonym: "Glycine hispida" EXACT [TyDI:52166]
-synonym: "Glycine max" EXACT [TyDI:52167]
-is_a: OBT:001247 ! pea family
-is_a: OBT:002780 ! cultivated Leguminosae
-
-[Term]
-id: OBT:003305
-name: student
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003306
-name: tilapia
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003307
-name: tomato-marinated broiler meat strip
-is_a: OBT:001629 ! marinated food
-is_a: OBT:002692 ! broiler meat strip
-
-[Term]
-id: OBT:003308
-name: traveler
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003309
-name: tuna
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003310
-name: turbot
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003311
-name: worker
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003312
-name: Alfalfa
-synonym: "Medicago sativa" EXACT [TyDI:53729]
-is_a: OBT:003277 ! Medicago
-
-[Term]
-id: OBT:003313
-name: bus driver
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003314
-name: chicken
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003315
-name: dairy livestock
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003316
-name: duck
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003317
-name: farmer
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003318
-name: goose
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003319
-name: hen
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003320
-name: horse
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003321
-name: medical staff
-synonym: "health care worker" EXACT [TyDI:53445]
-synonym: "medical personnel" RELATED [TyDI:53447]
-synonym: "medical professional" RELATED [TyDI:53446]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003322
-name: military service member
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003323
-name: polluted seawater
-is_a: OBT:000141 ! polluted environment
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003324
-name: prostitute
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003325
-name: quail
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003326
-name: saprophytic
-is_a: OBT:003282 ! chemoorganoheterotroph
-
-[Term]
-id: OBT:003327
-name: scientist
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003328
-name: slaughterer
-synonym: "slaughterman" EXACT [TyDI:53421]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003329
-name: swine
-synonym: "hog" RELATED [TyDI:53708]
-synonym: "porcine" RELATED [TyDI:53709]
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003330
-name: turkey
-is_a: OBT:003300 ! poultry
-
-[Term]
-id: OBT:003331
-name: veterinarian
-synonym: "veterinary surgeon" RELATED [TyDI:55964]
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003332
-name: welder
-is_a: OBT:003311 ! worker
-
-[Term]
-id: OBT:003333
-name: alkaline soda lake
-is_a: OBT:001399 ! alkaline lake
-is_a: OBT:002940 ! soda lake
-
-[Term]
-id: OBT:003334
-name: broiler chicken
-is_a: OBT:003314 ! chicken
-
-[Term]
-id: OBT:003335
-name: crude-oil-contaminated seawater
-is_a: OBT:003323 ! polluted seawater
-
-[Term]
-id: OBT:003336
-name: livestock boar
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003337
-name: pig
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003338
-name: researcher
-is_a: OBT:003327 ! scientist
-
-[Term]
-id: OBT:003339
-name: soldier
-is_a: OBT:003322 ! military service member
-
-[Term]
-id: OBT:003340
-name: sow
-is_a: OBT:003329 ! swine
-
-[Term]
-id: OBT:003341
-name: ABF pig
-is_a: OBT:003337 ! pig
-
-[Term]
-id: OBT:003342
-name: bedside water bottle
-is_a: OBT:001456 ! bottle
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003343
-name: fermented beverage
-is_a: OBT:001078 ! drink
-is_a: OBT:003046 ! fermented liquid
-
-[Term]
-id: OBT:003344
-name: fermented fruit
-is_a: OBT:001122 ! fruit and primary derivative thereof
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003345
-name: organic compound contaminated soil
-synonym: "carbon source enriched soil" EXACT [TyDI:53256]
-is_a: OBT:000874 ! site contaminated with organic compound
-is_a: OBT:003118 ! soil contaminated with industrial xenobiotic compound
-
-[Term]
-id: OBT:003346
-name: spring high in sulfide
-synonym: "sulfide-rich spring" EXACT [TyDI:53516]
-is_a: OBT:001333 ! spring
-is_a: OBT:003077 ! sulfide-rich water
-
-[Term]
-id: OBT:003347
-name: tzatziki
-is_a: OBT:000570 ! composite food
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003348
-name: PCB contaminated soil
-synonym: "soil percolated with PCP" RELATED [TyDI:53570]
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003349
-name: almond beverage
-is_a: OBT:001401 ! almond and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003350
-name: amaranth milk
-is_a: OBT:001403 ! amaranth and primary derivative thereof
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003351
-name: cashew beverage
-is_a: OBT:001475 ! cashew and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003352
-name: chili sauce
-is_a: OBT:001950 ! chili pepper and related product
-is_a: OBT:003022 ! sauce
-
-[Term]
-id: OBT:003353
-name: coconut beverage
-is_a: OBT:001495 ! coconut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003354
-name: cowpea beverage
-is_a: OBT:001696 ! pea and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003355
-name: fermented soybean
-is_a: OBT:001781 ! soybean and related product
-is_a: OBT:003047 ! fermented plant-based food
-
-[Term]
-id: OBT:003356
-name: guacamole
-is_a: OBT:001887 ! avocado and primary derivative thereof
-is_a: OBT:003022 ! sauce
-
-[Term]
-id: OBT:003357
-name: hazelnut beverage
-is_a: OBT:001590 ! hazelnut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003358
-name: hospital tap water
-is_a: OBT:002283 ! tap water
-is_a: OBT:002989 ! hospital drinking water
-
-[Term]
-id: OBT:003359
-name: hydrocarbon contaminated soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003360
-name: lupin beverage
-is_a: OBT:001622 ! lupin and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003361
-name: natural gas-enriched soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003362
-name: peanut beverage
-is_a: OBT:001697 ! peanut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003363
-name: pistachio beverage
-is_a: OBT:001717 ! pistachio and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003364
-name: quinoa beverage
-is_a: OBT:001734 ! quinoa and primary derivative thereof
-is_a: OBT:003054 ! grain based drink
-
-[Term]
-id: OBT:003365
-name: sewerage system
-is_a: OBT:000960 ! water transport structure
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003366
-name: soy beverage
-synonym: "soy drink" EXACT []
-synonym: "soy juice" EXACT []
-synonym: "soya beverage" EXACT []
-synonym: "soya drink" EXACT []
-synonym: "soya juice" EXACT []
-is_a: OBT:001781 ! soybean and related product
-is_a: OBT:003061 ! legume based drink
-
-[Term]
-id: OBT:003367
-name: sulfide-rich hot spring
-synonym: "hotspring high in sulfide" RELATED [TyDI:53332]
-is_a: OBT:003346 ! spring high in sulfide
-
-[Term]
-id: OBT:003368
-name: tea infusion
-is_a: OBT:001598 ! hot drink
-is_a: OBT:003059 ! leaf based drink
-
-[Term]
-id: OBT:003369
-name: vegetable puree
-is_a: OBT:001199 ! mashed food
-is_a: OBT:001499 ! cooked food
-is_a: OBT:001834 ! vegetable based dish
-
-[Term]
-id: OBT:003370
-name: walnut beverage
-is_a: OBT:001838 ! walnut and primary derivative thereof
-is_a: OBT:003064 ! nut based drink
-
-[Term]
-id: OBT:003371
-name: Balinese traditional fermented sausage
-synonym: "Urutan" EXACT [TyDI:52278]
-is_a: OBT:001758 ! sausage
-is_a: OBT:003094 ! fermented meat
-
-[Term]
-id: OBT:003372
-name: PAH contaminated soil
-synonym: "polycyclic aromatic hydrocarbon contaminated soil" EXACT [TyDI:53625]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003373
-name: almond milk
-is_a: OBT:003349 ! almond beverage
-
-[Term]
-id: OBT:003374
-name: cashew milk
-synonym: "cashew juice" RELATED [TyDI:52239]
-is_a: OBT:003351 ! cashew beverage
-
-[Term]
-id: OBT:003375
-name: caviar
-synonym: "sturgeon egg" EXACT [TyDI:53427]
-synonym: "sturgeon roe" EXACT [TyDI:53426]
-is_a: OBT:001277 ! raw seafood
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003376
-name: coconut milk
-is_a: OBT:003353 ! coconut beverage
-
-[Term]
-id: OBT:003377
-name: coconut water
-synonym: "coconut juice" RELATED [TyDI:51864]
-is_a: OBT:003353 ! coconut beverage
-
-[Term]
-id: OBT:003378
-name: cowpea milk
-is_a: OBT:003354 ! cowpea beverage
-
-[Term]
-id: OBT:003379
-name: creosote contaminated soil
-synonym: "creosote-contaminated soil" EXACT [TyDI:53436]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003380
-name: deer
-is_a: OBT:000967 ! wild animal
-is_a: OBT:001625 ! mammalian
-is_a: OBT:002589 ! ruminant
-
-[Term]
-id: OBT:003381
-name: fermented cheese
-is_a: OBT:001480 ! cheese
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003382
-name: flaxseed beverage
-synonym: "flax beverage" RELATED [TyDI:53535]
-is_a: OBT:001551 ! flaxseed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003383
-name: hazelnut milk
-is_a: OBT:003357 ! hazelnut beverage
-
-[Term]
-id: OBT:003384
-name: hempseed beverage
-synonym: "hemp beverage" RELATED [TyDI:53540]
-is_a: OBT:001593 ! hemp seed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003385
-name: landfill contaminated by PCB
-is_a: OBT:003348 ! PCB contaminated soil
-
-[Term]
-id: OBT:003386
-name: lupin milk
-is_a: OBT:003360 ! lupin beverage
-
-[Term]
-id: OBT:003387
-name: meju
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003388
-name: natto
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003389
-name: oil contaminated soil
-synonym: "oil impregnated soil" RELATED [TyDI:53403]
-synonym: "oil-contaminated soil" EXACT [TyDI:53402]
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003390
-name: peanut milk
-is_a: OBT:003362 ! peanut beverage
-
-[Term]
-id: OBT:003391
-name: pistachio milk
-is_a: OBT:003363 ! pistachio beverage
-
-[Term]
-id: OBT:003392
-name: quinate enriched soil
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003393
-name: quinoa milk
-is_a: OBT:003364 ! quinoa beverage
-
-[Term]
-id: OBT:003394
-name: salmon egg
-synonym: "ikura" RELATED [TyDI:51548]
-synonym: "salmon roe" EXACT [TyDI:51549]
-is_a: OBT:001277 ! raw seafood
-is_a: OBT:003149 ! fish roe and product thereof
-
-[Term]
-id: OBT:003395
-name: sesame beverage
-is_a: OBT:001768 ! sesame seed and primary derivative thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003396
-name: sewer
-is_a: OBT:003365 ! sewerage system
-
-[Term]
-id: OBT:003397
-name: sour cream
-is_a: OBT:001505 ! cream
-is_a: OBT:003093 ! fermented dairy product
-
-[Term]
-id: OBT:003398
-name: sourdough
-synonym: "naturally leavened bread dough" EXACT [TyDI:54041]
-is_a: OBT:001029 ! cereal and pseudo-cereal dough-based product
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003399
-name: soy milk
-synonym: "soya milk" EXACT []
-synonym: "soymilk" EXACT [TyDI:58411]
-is_a: OBT:003366 ! soy beverage
-
-[Term]
-id: OBT:003400
-name: storm drain
-synonym: " storm sewer" RELATED [TyDI:58049]
-synonym: "stormwater drain" RELATED [TyDI:58051]
-synonym: "surface water drain" RELATED [TyDI:58052]
-synonym: "surface-water drain" RELATED [TyDI:58050]
-is_a: OBT:003365 ! sewerage system
-
-[Term]
-id: OBT:003401
-name: sunflower beverage
-is_a: OBT:001805 ! sunflower seed and primary derivatives thereof
-is_a: OBT:003108 ! oleaginous seed based drink
-
-[Term]
-id: OBT:003402
-name: walnut milk
-is_a: OBT:003370 ! walnut beverage
-
-[Term]
-id: OBT:003403
-name: xylene contaminated soil
-is_a: OBT:003359 ! hydrocarbon contaminated soil
-
-[Term]
-id: OBT:003404
-name: yoghurt from fermented soybean milk
-synonym: "yoghurt from fermented soymilk" RELATED [TyDI:52603]
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003405
-name: barley beverage
-is_a: OBT:001893 ! barley and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003406
-name: brined cheese
-synonym: "pickled cheese" RELATED [TyDI:54953]
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003407
-name: chief sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003408
-name: chlorophenol-contaminated groundwater
-is_a: OBT:002467 ! ground water
-is_a: OBT:003042 ! contaminated groundwater
-
-[Term]
-id: OBT:003409
-name: contaminated soil with total petroleum hydrocarbon
-synonym: "contaminated soil with TPH" EXACT [TyDI:53454]
-is_a: OBT:003389 ! oil contaminated soil
-
-[Term]
-id: OBT:003410
-name: corn beverage
-is_a: OBT:002120 ! maize and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003411
-name: creosote wood preservative-contaminated soil
-is_a: OBT:003379 ! creosote contaminated soil
-
-[Term]
-id: OBT:003412
-name: dosa
-is_a: OBT:001744 ! rice based dish
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003413
-name: elk
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003414
-name: fermented dough
-is_a: OBT:001736 ! raw dough
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003415
-name: final sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003416
-name: flax milk
-is_a: OBT:003382 ! flaxseed beverage
-
-[Term]
-id: OBT:003417
-name: forest musk deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003418
-name: hemp milk
-is_a: OBT:003384 ! hempseed beverage
-
-[Term]
-id: OBT:003419
-name: kimchi
-is_a: OBT:002184 ! pickled food
-is_a: OBT:003096 ! fermented vegetable product
-
-[Term]
-id: OBT:003420
-name: laboratory sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003421
-name: leavened dough
-is_a: OBT:001736 ! raw dough
-is_a: OBT:003144 ! fermented cereal-based product
-
-[Term]
-id: OBT:003422
-name: moose
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003423
-name: oat beverage
-synonym: "oat drink" EXACT []
-synonym: "oat juice" EXACT []
-synonym: "oatly drink" NARROW []
-is_a: OBT:002154 ! oat and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003424
-name: phenanthrene contaminated soil
-synonym: "phenanthrene-contaminated soil" EXACT [TyDI:53351]
-is_a: OBT:003372 ! PAH contaminated soil
-
-[Term]
-id: OBT:003425
-name: red deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003426
-name: reindeer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003427
-name: rice beverage
-synonym: "rice drink" EXACT []
-synonym: "rice juice" EXACT []
-is_a: OBT:002223 ! rice and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003428
-name: ripened cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003429
-name: sesame milk
-is_a: OBT:003395 ! sesame beverage
-
-[Term]
-id: OBT:003430
-name: soil contaminated with used engine oil
-is_a: OBT:003389 ! oil contaminated soil
-
-[Term]
-id: OBT:003431
-name: spelt beverage
-is_a: OBT:002309 ! wheat and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003432
-name: streched curd cheese
-synonym: "pasta filata" EXACT [TyDI:55043]
-synonym: "plastic curd cheese" EXACT [TyDI:55042]
-synonym: "pulled-curd cheese" EXACT [TyDI:55041]
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003433
-name: sunflower milk
-is_a: OBT:003401 ! sunflower beverage
-
-[Term]
-id: OBT:003434
-name: teff beverage
-is_a: OBT:002285 ! teff and primary derivative thereof
-is_a: OBT:003087 ! cereal based drink
-
-[Term]
-id: OBT:003435
-name: traditional sourdough
-synonym: "artisan bakery sourdough" EXACT [TyDI:51170]
-synonym: "artisanal sourdough" EXACT [TyDI:51173]
-synonym: "natural fermented sourdough" EXACT [TyDI:51174]
-synonym: "natural sourdough" EXACT [TyDI:51169]
-synonym: "naturally fermented sourdough" EXACT [TyDI:51176]
-synonym: "spontaneous sourdough" EXACT [TyDI:51171]
-synonym: "spontaneously fermented sourdough" EXACT [TyDI:51172]
-synonym: "traditionnal sourdough" EXACT [TyDI:51175]
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003436
-name: type I sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003437
-name: type II sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003438
-name: type III sourdough
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003439
-name: warm seawater
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:003105 ! marine water
-
-[Term]
-id: OBT:003440
-name: whey cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003441
-name: white tail deer
-is_a: OBT:003380 ! deer
-
-[Term]
-id: OBT:003442
-name: barley milk
-is_a: OBT:003405 ! barley beverage
-
-[Term]
-id: OBT:003443
-name: brocciu
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003444
-name: caciocavallo
-is_a: OBT:003432 ! streched curd cheese
-
-[Term]
-id: OBT:003445
-name: chemolithoheterotroph
-synonym: "chemo lithoheterotroph " EXACT [TyDI:54334]
-is_a: OBT:002895 ! chemoheterotroph
-is_a: OBT:002896 ! chemolithotroph
-
-[Term]
-id: OBT:003446
-name: contaminated aquifer
-is_a: OBT:002687 ! aquifer
-is_a: OBT:003042 ! contaminated groundwater
-
-[Term]
-id: OBT:003447
-name: corn milk
-is_a: OBT:003410 ! corn beverage
-
-[Term]
-id: OBT:003448
-name: feta
-is_a: OBT:003406 ! brined cheese
-
-[Term]
-id: OBT:003449
-name: frozen yogurt
-is_a: OBT:001564 ! frozen food
-is_a: OBT:003241 ! yogurt
-
-[Term]
-id: OBT:003450
-name: hard cheese
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003451
-name: man
-is_a: OBT:001192 ! male animal
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003452
-name: mozzarella
-is_a: OBT:003432 ! streched curd cheese
-
-[Term]
-id: OBT:003453
-name: newborn infant
-synonym: "neonatal animal" EXACT [TyDI:53896]
-synonym: "neonate" EXACT [TyDI:53897]
-synonym: "newborn" EXACT [TyDI:53898]
-is_a: OBT:001662 ! newborn animal
-is_a: OBT:003184 ! baby
-
-[Term]
-id: OBT:003454
-name: oat milk
-synonym: "oatmilk" EXACT []
-is_a: OBT:003423 ! oat beverage
-
-[Term]
-id: OBT:003455
-name: rice milk
-synonym: "ricemilk" EXACT []
-is_a: OBT:003427 ! rice beverage
-
-[Term]
-id: OBT:003456
-name: ricotta
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003457
-name: schabziger
-synonym: "sapsago" EXACT [TyDI:55029]
-synonym: "sérac" EXACT [TyDI:55030]
-is_a: OBT:003440 ! whey cheese
-
-[Term]
-id: OBT:003458
-name: semi soft cheese
-synonym: "semi hard cheese" EXACT [TyDI:55022]
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003459
-name: soft cheese
-is_a: OBT:003428 ! ripened cheese
-
-[Term]
-id: OBT:003460
-name: spelt milk
-is_a: OBT:003431 ! spelt beverage
-
-[Term]
-id: OBT:003461
-name: teff milk
-is_a: OBT:003434 ! teff beverage
-
-[Term]
-id: OBT:003462
-name: warm coastal water
-is_a: OBT:002019 ! environmental water with physical property
-is_a: OBT:003132 ! coastal water
-
-[Term]
-id: OBT:003463
-name: woman
-is_a: OBT:001103 ! female animal
-is_a: OBT:003245 ! adult human
-
-[Term]
-id: OBT:003464
-name: yeast bread dough
-is_a: OBT:003414 ! fermented dough
-
-[Term]
-id: OBT:003465
-name: Beaufort
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003466
-name: Brick cheese
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003467
-name: Caciocavallo
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003468
-name: Cantal
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003469
-name: Cheddar
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003470
-name: Comté
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003471
-name: Emmental
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003472
-name: Fontina
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003473
-name: Formaggio di Fossa
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003474
-name: Gouda
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003475
-name: Granular cheese
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003476
-name: Gruyère
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003477
-name: Laguiole
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003478
-name: Leerdammer
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003479
-name: Morbier
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003480
-name: Raclette
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003481
-name: Toma
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003482
-name: Trappist
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003483
-name: Valtellina Casera
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003484
-name: aquifer contaminated with unleaded gasoline
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003485
-name: arsenic-rich aquifer
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003486
-name: blue veined cheese
-is_a: OBT:003458 ! semi soft cheese
-
-[Term]
-id: OBT:003487
-name: cauliflower
-is_a: OBT:001391 ! Brassica
-is_a: OBT:003255 ! cultivated crucifer
-
-[Term]
-id: OBT:003488
-name: chloroethene-contaminated aquifer
-is_a: OBT:003446 ! contaminated aquifer
-
-[Term]
-id: OBT:003489
-name: extra hard cheese
-is_a: OBT:003450 ! hard cheese
-
-[Term]
-id: OBT:003490
-name: goat
-is_a: OBT:001103 ! female animal
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003491
-name: mother
-is_a: OBT:003463 ! woman
-
-[Term]
-id: OBT:003492
-name: mould ripened cheese
-is_a: OBT:003459 ! soft cheese
-
-[Term]
-id: OBT:003493
-name: pregnant woman
-is_a: OBT:003463 ! woman
-
-[Term]
-id: OBT:003494
-name: smear ripened cheese
-is_a: OBT:003459 ! soft cheese
-
-[Term]
-id: OBT:003495
-name: Asiago
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003496
-name: Bleu
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003497
-name: Blue Wensleydate
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003498
-name: Brie
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003499
-name: Buche de chèvre
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003500
-name: Camembert
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003501
-name: Carré de l'est
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003502
-name: Danablu
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003503
-name: Epoisses
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003504
-name: Gorgonzola
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003505
-name: Gubbeen
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003506
-name: Hand cheese
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003507
-name: Langres
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003508
-name: Liederkranz
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003509
-name: Limburger
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003510
-name: Livarot
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003511
-name: Maroilles
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003512
-name: Munster
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003513
-name: Neufchatel
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003514
-name: Parmesan
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003515
-name: Pont l'Evêque
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003516
-name: Reblochon
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003517
-name: Romano
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003518
-name: Roquefort
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003519
-name: Saint-Nectaire
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003520
-name: Saint-Paulin
-synonym: "Saint Paulin" EXACT [TyDI:50048]
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003521
-name: Sapsago
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003522
-name: Scimudin
-is_a: OBT:003492 ! mould ripened cheese
-
-[Term]
-id: OBT:003523
-name: Spalen
-is_a: OBT:003489 ! extra hard cheese
-
-[Term]
-id: OBT:003524
-name: Stilton
-is_a: OBT:003486 ! blue veined cheese
-
-[Term]
-id: OBT:003525
-name: Taleggio
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003526
-name: Tilsit
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003527
-name: romadur
-is_a: OBT:003494 ! smear ripened cheese
-
-[Term]
-id: OBT:003528
-name: working horse
-is_a: OBT:001384 ! working animal
-is_a: OBT:003320 ! horse
-
-[Term]
-id: OBT:003529
-name: decaying leaf litter
-is_a: OBT:002912 ! leaf litter
-is_a: OBT:003090 ! decaying leaf
-
-[Term]
-id: OBT:003530
-name: plant based juice
-synonym: "plant milk" RELATED [TyDI:53655]
-is_a: OBT:003013 ! plant based drink
-is_a: OBT:003058 ! juice
-
-[Term]
-id: OBT:003531
-name: sheep
-synonym: "ovin" RELATED [TyDI:54422]
-is_a: OBT:002078 ! herbivore
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003532
-name: cattle
-is_a: OBT:002589 ! ruminant
-is_a: OBT:003295 ! mammalian livestock
-
-[Term]
-id: OBT:003533
-name: fermented tea leaf
-is_a: OBT:003047 ! fermented plant-based food
-is_a: OBT:003059 ! leaf based drink
-
-[Term]
-id: OBT:003534
-name: fruit based juice
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003535
-name: garlic oil
-is_a: OBT:001044 ! condiment
-is_a: OBT:002058 ! garlic and related product
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003536
-name: olive oil
-is_a: OBT:002980 ! edible oil and related product
-is_a: OBT:003109 ! olive and primary derivative thereof
-
-[Term]
-id: OBT:003537
-name: sourdough starter
-synonym: "commercial sourdough" EXACT [TyDI:50927]
-synonym: "selected sourdough" EXACT [TyDI:50926]
-synonym: "sourdough bread starter" EXACT [TyDI:50925]
-is_a: OBT:000432 ! starter culture
-is_a: OBT:003398 ! sourdough
-
-[Term]
-id: OBT:003538
-name: thyme oil
-is_a: OBT:001044 ! condiment
-is_a: OBT:002291 ! thyme and related product
-is_a: OBT:002980 ! edible oil and related product
-
-[Term]
-id: OBT:003539
-name: vegetable based juice
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003540
-name: Fuzhuan brick tea
-synonym: "Fu brick tea" EXACT [TyDI:50042]
-synonym: "Fu-zhuan brick tea" EXACT [TyDI:50043]
-is_a: OBT:003533 ! fermented tea leaf
-
-[Term]
-id: OBT:003541
-name: beer
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003542
-name: bovine
-is_a: OBT:003532 ! cattle
-
-[Term]
-id: OBT:003543
-name: cider
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003544
-name: sugar cane juice
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003545
-name: waste water pipe
-synonym: "waste pipe" RELATED [TyDI:53903]
-is_a: OBT:003033 ! water pipe
-is_a: OBT:003174 ! wastewater treatment equipment
-
-[Term]
-id: OBT:003546
-name: wine
-is_a: OBT:001397 ! alcoholic drink
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003547
-name: Bristish beer
-is_a: OBT:003541 ! beer
-
-[Term]
-id: OBT:003548
-name: apple cider
-is_a: OBT:003543 ! cider
-
-[Term]
-id: OBT:003549
-name: beef cattle
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003550
-name: beer Shava
-is_a: OBT:003541 ! beer
-
-[Term]
-id: OBT:003551
-name: bison
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003552
-name: buffalo
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003553
-name: marine farm fish
-is_a: OBT:002903 ! farmed fish
-is_a: OBT:003264 ! marine fish
-
-[Term]
-id: OBT:003554
-name: submarine hotspring
-is_a: OBT:002990 ! hotspring
-is_a: OBT:003274 ! submarine thermal spring
-
-[Term]
-id: OBT:003555
-name: fermented dry sausage
-is_a: OBT:003094 ! fermented meat
-is_a: OBT:003195 ! dry sausage
-
-[Term]
-id: OBT:003556
-name: fermented fresh cheese
-is_a: OBT:002043 ! fresh cheese
-is_a: OBT:003381 ! fermented cheese
-
-[Term]
-id: OBT:003557
-name: French dry sausage
-synonym: "saucisson" RELATED [TyDI:52117]
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003558
-name: Greek sausage
-synonym: "Greek salami" RELATED [TyDI:52265]
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003559
-name: cream cheese
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003560
-name: faisselle
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003561
-name: fromage blanc
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003562
-name: fuet
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003563
-name: salami
-is_a: OBT:003555 ! fermented dry sausage
-
-[Term]
-id: OBT:003564
-name: petit-suisse
-is_a: OBT:003561 ! fromage blanc
-
-[Term]
-id: OBT:003565
-name: vinegar
-is_a: OBT:000711 ! liquid food
-is_a: OBT:001044 ! condiment
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003566
-name: ewe
-is_a: OBT:001103 ! female animal
-is_a: OBT:003531 ! sheep
-
-[Term]
-id: OBT:003567
-name: malt vinegar
-synonym: "Alegar" EXACT [TyDI:53327]
-is_a: OBT:003565 ! vinegar
-
-[Term]
-id: OBT:003568
-name: rice vinegar
-is_a: OBT:003565 ! vinegar
-
-[Term]
-id: OBT:003569
-name: lamb
-is_a: OBT:001849 ! young animal
-is_a: OBT:003531 ! sheep
-
-[Term]
-id: OBT:003570
-name: soy sauce
-is_a: OBT:003022 ! sauce
-is_a: OBT:003355 ! fermented soybean
-
-[Term]
-id: OBT:003571
-name: bull
-is_a: OBT:001192 ! male animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003572
-name: cow
-synonym: "cows" EXACT [TyDI:54619]
-is_a: OBT:001103 ! female animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003573
-name: fermented table olive
-is_a: OBT:003109 ! olive and primary derivative thereof
-is_a: OBT:003344 ! fermented fruit
-
-[Term]
-id: OBT:003574
-name: mabisi
-is_a: OBT:003093 ! fermented dairy product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003575
-name: apple juice
-is_a: OBT:001879 ! apple and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003576
-name: beet juice
-synonym: "  beetroot juice" RELATED [TyDI:53346]
-is_a: OBT:001900 ! beetroot and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003577
-name: calf
-is_a: OBT:001849 ! young animal
-is_a: OBT:003542 ! bovine
-
-[Term]
-id: OBT:003578
-name: carrot juice
-is_a: OBT:001934 ! carrot and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003579
-name: celery juice
-is_a: OBT:001940 ! celery leaf and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003580
-name: chibwantu
-is_a: OBT:003144 ! fermented cereal-based product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003581
-name: cranberry juice
-is_a: OBT:001979 ! cranberry and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003582
-name: cucumber juice
-is_a: OBT:001981 ! cucumber and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003583
-name: grape juice
-is_a: OBT:002066 ! grape and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003584
-name: lemon juice
-is_a: OBT:002103 ! lemon and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003585
-name: orange juice
-is_a: OBT:002162 ! orange and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003586
-name: pineapple juice
-is_a: OBT:002188 ! pineapple and primary derivative thereof
-is_a: OBT:003534 ! fruit based juice
-
-[Term]
-id: OBT:003587
-name: tomato juice
-is_a: OBT:002293 ! tomato and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003588
-name: turnip juice
-synonym: "shalgam juice" RELATED [TyDI:51718]
-is_a: OBT:002297 ! turnip and related product
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003589
-name: wheatgrass juice
-is_a: OBT:002309 ! wheat and primary derivative thereof
-is_a: OBT:003539 ! vegetable based juice
-
-[Term]
-id: OBT:003590
-name: acetamide enriched soil
-is_a: OBT:003204 ! herbicide enriched soil
-is_a: OBT:003345 ! organic compound contaminated soil
-
-[Term]
-id: OBT:003591
-name: decaying leaf litter from a pine forest
-is_a: OBT:002925 ! pine litter
-is_a: OBT:003529 ! decaying leaf litter
-
-[Term]
-id: OBT:003592
-name: fermented cottage cheese
-is_a: OBT:002408 ! cottage cheese
-is_a: OBT:003556 ! fermented fresh cheese
-
-[Term]
-id: OBT:003593
-name: metata ayib
-is_a: OBT:003592 ! fermented cottage cheese
-
-[Term]
-id: OBT:003594
-name: dairy goat
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003490 ! goat
-
-[Term]
-id: OBT:003595
-name: pozol
-is_a: OBT:002120 ! maize and primary derivative thereof
-is_a: OBT:003144 ! fermented cereal-based product
-is_a: OBT:003343 ! fermented beverage
-
-[Term]
-id: OBT:003596
-name: fermented juice
-is_a: OBT:003343 ! fermented beverage
-is_a: OBT:003530 ! plant based juice
-
-[Term]
-id: OBT:003597
-name: fermented Elaeis Palm sap
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003598
-name: dairy sheep
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003566 ! ewe
-
-[Term]
-id: OBT:003599
-name: dairy cow
-synonym: "dairy cattle" RELATED [TyDI:54584]
-synonym: "dairy cows" EXACT [TyDI:54585]
-is_a: OBT:003315 ! dairy livestock
-is_a: OBT:003572 ! cow
-
-[Term]
-id: OBT:003600
-name: fermented cabbage juice
-is_a: OBT:002075 ! head cabbage and related product
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003601
-name: tejuino
-synonym: "tejuíno" EXACT [TyDI:51685]
-is_a: OBT:003410 ! corn beverage
-is_a: OBT:003596 ! fermented juice
-
-[Term]
-id: OBT:003602
-name: airway epithelium
-is_a: OBT:000408 ! respiratory tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003603
-name: chicken breast meat
-is_a: OBT:002394 ! chicken meat
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003604
-name: turkey breast meat
-is_a: OBT:002631 ! turkey meat
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003605
-name: rice bran
-is_a: OBT:001458 ! bran
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003606
-name: lacrimal sac
-is_a: OBT:000277 ! eye part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003607
-name: conjunctival sac
-is_a: OBT:000277 ! eye part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003608
-name: aneurysmal sac
-synonym: "aneurysm sac" EXACT []
-synonym: "aortic sac" EXACT []
-is_a: OBT:000231 ! circulatory system part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003609
-name: abdominal air sac
-synonym: "air sac" EXACT []
-synonym: "thoracic air sac" EXACT []
-is_a: OBT:000408 ! respiratory tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003610
-name: hernial sac
-is_a: OBT:000039 ! animal part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003611
-name: umbilical cord
-is_a: OBT:000463 ! urogenital tract part
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003612
-name: umbilical cord blood
-is_a: OBT:000521 ! blood
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003613
-name: vocal cord
-is_a: OBT:000529 ! broncho-pulmonary segment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003614
-name: cord-shaped
-is_a: OBT:000386 ! phenotype wrt shape
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003615
-name: box lunch
-is_a: OBT:000788 ! packed lunch
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003617
-name: environmental surface
-is_a: OBT:000006 ! artificial environment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003618
-name: ceramic tile
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003619
-name: ceramic wall tile
-is_a: OBT:003618 ! ceramic tile
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003620
-name: ceramic roofing tile
-is_a: OBT:003618 ! ceramic tile
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003621
-name: stainless steel surface
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003622
-name: PCV surface
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003623
-name: plasticized PVC
-synonym: "PVC plastic" NARROW []
-is_a: OBT:003622 ! PCV surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003624
-name: PVC film
-is_a: OBT:000787 ! packaging
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003625
-name: sealed concrete
-is_a: OBT:003617 ! environmental surface
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003626
-name: bamboo cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003627
-name: wood Cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003628
-name: plastic cutting board
-is_a: OBT:000582 ! cutting board
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003629
-name: voice prosthesis
-is_a: OBT:003630 ! tracheoesophageal prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003630
-name: tracheoesophageal prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003631
-name: silicone rubber voice prosthesis
-is_a: OBT:003629 ! voice prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003632
-name: prosthetic cardiac device
-synonym: "intracardiac prosthesis" NARROW []
-synonym: "prosthetic cardiovascular device" NARROW []
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003633
-name: prosthetic heart valve
-synonym: "heart valve prosthesis" NARROW []
-synonym: "prosthetic valve" NARROW []
-synonym: "valvular prosthesis" NARROW []
-is_a: OBT:003632 ! prosthetic cardiac device
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003634
-name: mitral valve prosthesis
-synonym: "mitral prosthesis" EXACT []
-is_a: OBT:003633 ! prosthetic heart valve
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003635
-name: aortic prosthetic valve
-synonym: "aortic valve prosthesis" EXACT []
-synonym: "arterial prosthesis" EXACT []
-is_a: OBT:003632 ! prosthetic cardiac device
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003636
-name: orthopedic prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003637
-name: othopedic implant
-is_a: OBT:003636 ! orthopedic prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003638
-name: hip prosthesis
-synonym: "prosthetic hip joint" EXACT []
-is_a: OBT:000830 ! prosthetic joint
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003639
-name: femoral prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003640
-name: knee prosthesis
-is_a: OBT:000830 ! prosthetic joint
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003641
-name: shoulder prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003642
-name: cranial prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003643
-name: penile prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003644
-name: testicular prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003645
-name: ocular prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003646
-name: prosthetic eye
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003647
-name: iris prosthesis
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003648
-name: orbital implant
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003649
-name: cochlear implant
-is_a: OBT:003645 ! ocular prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003650
-name: dental implant
-is_a: OBT:000591 ! dental prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003651
-name: palatal obturator prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003652
-name: breast prosthesis
-synonym: "mammary prosthesis" EXACT []
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003653
-name: breast implant
-is_a: OBT:003652 ! breast prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003654
-name: suction-socket prosthesis
-is_a: OBT:000398 ! prosthesis
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003655
-name: granular sludge
-is_a: OBT:001523 ! digester sludge
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003656
-name: aerobic granular sludge
-is_a: OBT:001861 ! anaerobic digester sludge
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003657
-name: aerobic granular sludge reactor
-synonym: "AGS reactor" EXACT []
-is_a: OBT:000180 ! aerobic bioreactor
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003658
-name: granular sludge bed reactor
-synonym: "EGSB reactor" EXACT []
-is_a: OBT:000488 ! anaerobic sludge blanket reactor
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003659
-name: public swimming bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003660
-name: indoor swimming bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003661
-name: shower bath
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003662
-name: public bath
-is_a: OBT:002203 ! public bathing facility
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003663
-name: traditional public bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003664
-name: bath basin
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003665
-name: thermal bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003666
-name: thermal saline bath
-is_a: OBT:002592 ! saline water
-is_a: OBT:003665 ! thermal bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003667
-name: mineral bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003668
-name: spa bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003669
-name: seawater bath
-is_a: OBT:003105 ! marine water
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003670
-name: freshwater bath
-is_a: OBT:002455 ! freshwater
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003671
-name: open air bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003672
-name: spring bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003673
-name: hot water bath
-is_a: OBT:003662 ! public bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003674
-name: hot spring bath
-is_a: OBT:002990 ! hotspring
-is_a: OBT:003673 ! hot water bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003675
-name: hot spring spa bath
-is_a: OBT:003674 ! hot spring bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003676
-name: bath sponge
-is_a: OBT:000208 ! bathroom equipment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003677
-name: bath tub heating
-is_a: OBT:000671 ! home heating system
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003678
-name: antiseptic bath
-is_a: OBT:000109 ! medical product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003679
-name: chlorhexidine bath
-is_a: OBT:003678 ! antiseptic bath
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003680
-name: veterinary product
-is_a: OBT:000011 ! medical environment
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003681
-name: insecticide bath
-is_a: OBT:003680 ! veterinary product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003682
-name: antiseptic shower
-is_a: OBT:000109 ! medical product
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003683
-name: dyeing bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003684
-name: skin tannery bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003685
-name: bleach bath
-is_a: OBT:000322 ! industrial chemical
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003689
-name: mango tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003690
-name: lemon tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003691
-name: peach tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003692
-name: apricot tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003693
-name: quince tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003694
-name: cherry tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003695
-name: khaki tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003696
-name: lime tree
-is_a: OBT:001567 ! fruit tree
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T18:51:57Z
-
-[Term]
-id: OBT:003697
-name: carrot plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003698
-name: broccoli plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003699
-name: brussel sprout plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003700
-name: chinese cabbage plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003701
-name: collard green plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003702
-name: head cabbage plant
-is_a: OBT:001391 ! Brassica
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003703
-name: shallot plant
-is_a: OBT:001389 ! Allium
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003704
-name: fruiting vegetable plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003705
-name: courgette plant
-synonym: "zucchini plant" EXACT []
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003706
-name: cucumber plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003707
-name: gherkin plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003708
-name: melon plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003709
-name: pumpkin plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003710
-name: sweet pepper plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003711
-name: watermelon plant
-is_a: OBT:003704 ! fruiting vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003712
-name: leafy vegetable plant
-is_a: OBT:001632 ! market garden plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003713
-name: celery plant
-is_a: OBT:003712 ! leafy vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003714
-name: spinach plant
-is_a: OBT:003712 ! leafy vegetable plant
-created_by: Claire_Nedellec
-creation_date: 2020-10-27T12:51:57Z
-
-[Term]
-id: OBT:003715
-name: table water
-is_a: OBT:001530 ! drinking water
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003716
-name: garment factory
-is_a: OBT:001818 ! textile mill
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003717
-name: dyeing factory
-is_a: OBT:001818 ! textile mill
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003718
-name: traditional Chinese fermented cabbage
-is_a: OBT:002321 ! Chinese cabbage
-is_a: OBT:003096 ! fermented vegetable product
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003719
-name: nasal swab
-is_a: OBT:001228 ! nasal secretion
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003720
-name: rum factory
-is_a: OBT:002039 ! food fermentation factory
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003721
-name: whisky distillery
-is_a: OBT:002039 ! food fermentation factory
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003722
-name: liquor
-is_a: OBT:001397 ! alcoholic drink
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003723
-name: udder
-is_a: OBT:000723 ! mammalian part
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003724
-name: lactic starter
-is_a: OBT:000584 ! dairy starter culture
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003726
-name: plant residue from food processing
-is_a: OBT:001558 ! food processing waste
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003727
-name: grape pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003728
-name: apple pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003729
-name: olive pomace
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003730
-name: grape must
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003731
-name: sugarcane bagasse
-synonym: "sugar cane bagasse" EXACT []
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003732
-name: agave bagasse
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003733
-name: citrus bagasse
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003734
-name: soy bran
-is_a: OBT:000038 ! animal feed
-created_by: Claire_Nedellec
-creation_date: 2020-10-30T12:51:57Z
-
-[Term]
-id: OBT:003735
-name: palm kernel press cake
-synonym: "residue from palm oil extraction" NARROW []
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003736
-name: sugar beet pressed pulp
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003737
-name: cranberry press cake
-is_a: OBT:001558 ! food processing waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003738
-name: forage residue
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003739
-name: cotton plant waste
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003740
-name: cottonseed hull
-is_a: OBT:001718 ! agricultural plant residue
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003741
-name: olive press cake
-is_a: OBT:003726 ! plant residue from food processing
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003742
-name: wood waste
-is_a: OBT:000467 ! waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003743
-name: sawdust
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003744
-name: waste house wood
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003745
-name: construction wood waste
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003746
-name: demolition wood waste
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003747
-name: hazardous industrial waste
-is_a: OBT:000685 ! industrial waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003748
-name: agricultural woody waste
-is_a: OBT:000478 ! agricultural waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003749
-name: wood waste fiber
-is_a: OBT:003742 ! wood waste
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003750
-name: transport structure
-is_a: OBT:000162 ! transport equipment
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003751
-name: pallet
-is_a: OBT:003750 ! transport structure
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003752
-name: shipping container
-is_a: OBT:003750 ! transport structure
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003753
-name: wooden pallet
-is_a: OBT:003751 ! pallet
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003756
-name: wood barrel
-is_a: OBT:000434 ! storage equipment
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003757
-name: oak barrel
-is_a: OBT:003756 ! wood barrel
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003759
-name: bakery
-is_a: OBT:001557 ! food processing factory
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003760
-name: traditional bakery
-is_a: OBT:003759 ! bakery
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003761
-name: traditional dairy
-is_a: OBT:001988 ! dairy processing plant
-created_by: Claire_Nedellec
-creation_date: 2020-11-03T10:10:57Z
-
-[Term]
-id: OBT:003762
-name: dairy farm
-is_a: OBT:001988 ! dairy processing plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003763
-name: snowpack
-is_a: OBT:000881 ! snow
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003764
-name: conifer needle
-is_a: OBT:000807 ! phylloplane part
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003765
-name: agricultural fence
-is_a: OBT:001183 ! livestock habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003766
-name: ungulate
-is_a: OBT:002078 ! herbivore
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003767
-name: biome type forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003768
-name: alpine forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003769
-name: tropical rain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003770
-name: arid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003771
-name: boreal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003772
-name: coastal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003773
-name: cooler rain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003774
-name: dune forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003775
-name: equatorial forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003776
-name: montane forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003777
-name: hemiboreal forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003778
-name: high altitude forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003779
-name: humid lakeland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003780
-name: low mountain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003781
-name: subtropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003782
-name: taiga forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003783
-name: lowland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003784
-name: marshy forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003785
-name: mountain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003786
-name: neotropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003787
-name: paleotropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003788
-name: savannah - forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003789
-name: subalpine forest
-synonym: "sub-alpine forest" EXACT []
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003790
-name: sub-Antarctic forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003791
-name: warm sub-tropical forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003792
-name: dry forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003793
-name: semi - arid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003794
-name: semiarid temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003795
-name: hill forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003796
-name: hot forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003797
-name: humid forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003798
-name: inland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003799
-name: moist forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003800
-name: plain forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003801
-name: pluvial forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003802
-name: riverbank forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003803
-name: riverine forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003804
-name: submerged forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003805
-name: temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003806
-name: underwater forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003807
-name: upland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003808
-name: volcanic forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003809
-name: warm - temperate forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003810
-name: wet forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003811
-name: wildland forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003812
-name: drained forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003813
-name: soddy forest
-is_a: OBT:003767 ! biome type forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003814
-name: natural and managed forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T12:10:57Z
-
-[Term]
-id: OBT:003815
-name: natural forest
-is_a: OBT:003814 ! natural and managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003816
-name: virgin forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003817
-name: uncontrolled forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003818
-name: undisturbed forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003819
-name: unmanaged forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003820
-name: unpolluted forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003821
-name: preserved forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003822
-name: protected forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003823
-name: native forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003824
-name: intact forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003825
-name: primary forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003826
-name: primeval forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003827
-name: pristine area of native forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003828
-name: pristine forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003829
-name: non-burnt forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003830
-name: unburnt forest
-is_a: OBT:003815 ! natural forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003831
-name: managed forest
-is_a: OBT:003814 ! natural and managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003832
-name: man - made forest system
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003833
-name: municipal forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003834
-name: park forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003836
-name: periurban forest
-synonym: "peri-urban" EXACT []
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003837
-name: plantation forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003838
-name: recreational forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003839
-name: reserve forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003840
-name: rural forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003841
-name: semi-natural forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003842
-name: suburban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003843
-name: urban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003844
-name: village-adjacent forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003845
-name: village forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003846
-name: wood forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003847
-name: second-growth forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003848
-name: secondary forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003849
-name: early successional forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003850
-name: burnt forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003851
-name: artificial forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003852
-name: commercial forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003853
-name: commercial plantation forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003854
-name: community forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003855
-name: disturbed forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003856
-name: disturbed urban forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003857
-name: historical forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003858
-name: human disturbed forest
-is_a: OBT:003831 ! managed forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:08:57Z
-
-[Term]
-id: OBT:003859
-name: old forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003860
-name: mature forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003861
-name: mature forest of high conservation value
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003862
-name: mature old-growth forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003863
-name: young forest
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003864
-name: forest of given species
-is_a: OBT:001119 ! forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003865
-name: alder forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003866
-name: angiosperm-dominated forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003867
-name: arboreal forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003868
-name: argan forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003869
-name: aspen forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003870
-name: beach forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003871
-name: beech forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003872
-name: beech-dominated forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003873
-name: birch forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003874
-name: boreonemoral forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003875
-name: bosque forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003876
-name: broad-leaved forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003877
-name: broadleaf forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003878
-name: Cercocarpus forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003879
-name: chestnut forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003880
-name: cloud forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003881
-name: conifer forest
-synonym: "coniferous forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003883
-name: coppice forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003884
-name: cypress forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003885
-name: deciduous forest
-synonym: "deciduous specie forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003886
-name: deciduous dipterocarp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003888
-name: herb-rich coniferous forest
-is_a: OBT:003881 ! conifer forest
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003890
-name: dipterocarp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003892
-name: evergreen broad-leaved forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003893
-name: forest with dominant vegetation
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003894
-name: hardwood forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003896
-name: holm-oak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003897
-name: kelp forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003898
-name: larch forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003899
-name: lucidophyllous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003900
-name: mangrove forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003901
-name: maple forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003902
-name: maso bamboo forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003903
-name: hemlock fir forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003904
-name: amabilis fir forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003906
-name: monodominant forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003907
-name: monospecific forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003908
-name: spruce forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003909
-name: Nothofagaceae forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003910
-name: Nothofagus forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003911
-name: oak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003912
-name: oak-hickory forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003914
-name: ombrophilous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003916
-name: papyrifera forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003917
-name: perennial forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003918
-name: riparian forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003919
-name: pure forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003920
-name: red pine forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003921
-name: redwood forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003922
-name: riparian woodland
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003923
-name: poplar forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003924
-name: sclerophyll forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003925
-name: seasonal dry tropical forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003926
-name: scrub forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003927
-name: semi-evergreen forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003928
-name: semideciduous forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003929
-name: stone pine forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003931
-name: tanoak forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003932
-name: xeric forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003933
-name: xerophytic forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003934
-name: mix forest
-synonym: "mixed forest" EXACT []
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-[Term]
-id: OBT:003935
-name: papilionoid legume tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003936
-name: leguminous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003937
-name: tulip tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003938
-name: tea-oil tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003939
-name: tea plant
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003940
-name: Syzygiumcordatum tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003941
-name: shea butter tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003942
-name: rubber tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003943
-name: riparian tree specie
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003944
-name: Protea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003945
-name: Prosopis tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003946
-name: peepal tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003947
-name: Pandanus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003948
-name: pacara earpod tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003949
-name: Olea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003950
-name: Nothofagus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003951
-name: mopane tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003952
-name: Masson pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003953
-name: manuka tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003954
-name: loquat tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003955
-name: lodgepole pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003956
-name: lacquer tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003957
-name: Katsura tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003958
-name: kassod tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003959
-name: Hippophae tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003960
-name: dipterocarp tree
-synonym: "Dipterocarpaceae tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003961
-name: Dekopon tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003962
-name: cycad tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003963
-name: cupuassu tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003964
-name: cupressaceous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003965
-name: chitalpa tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003966
-name: chinquapin tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003967
-name: Casuarina tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003968
-name: Ascomycota tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003969
-name: Alnus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003970
-name: Allocasuarina tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003971
-name: South-African Protea tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003972
-name: African leguminous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003973
-name: willow tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003974
-name: wild tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003976
-name: whitebark pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003977
-name: White spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003978
-name: white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003979
-name: white oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003980
-name: walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003981
-name: urban tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003982
-name: Ulmus nigra tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003983
-name: Ulmus Dodoens Elm
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003984
-name: turkey oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003985
-name: tung tree
-synonym: "tung oil tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003986
-name: tanoak tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003987
-name: Talh tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003988
-name: sycamore tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003989
-name: sweet chestnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003990
-name: Swedish spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003991
-name: sudden oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003992
-name: stone pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003993
-name: silver birch
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003994
-name: silk oak
-synonym: "silk oak tree" EXACT []
-is_a: OBT:001666 ! oak
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003995
-name: Sebertia acuminata
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003996
-name: scot pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003997
-name: riparian Alnus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003998
-name: Rhodococcus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:003999
-name: redwood tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004001
-name: radiata pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004002
-name: Quercus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004003
-name: pygmy tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004004
-name: prunus tree
-synonym: "Prunus spp. tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004005
-name: poplar tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004006
-name: ponderosa pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004007
-name: pomegranate tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004008
-name: pome tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004009
-name: poison oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004010
-name: pistachio tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004011
-name: pinyon pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004012
-name: persimmon tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004013
-name: persian walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004014
-name: pepper tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004015
-name: pecan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004016
-name: Paulownia tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004017
-name: palm tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004018
-name: ornamental tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004019
-name: ornamental Prunus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004020
-name: orchard tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004021
-name: Gingko tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004022
-name: nutmeg tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004023
-name: nutgall tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004024
-name: norway spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004025
-name: North American white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004026
-name: North American oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004027
-name: needled white pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004028
-name: needle pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004029
-name: Monterey pine
-synonym: "insignis pine" EXACT []
-synonym: "radiata pine" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004030
-name: Mongolian pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004031
-name: medlar tree
-synonym: "Mespilus germanica" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004032
-name: Mediterranean oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004033
-name: Maritime pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004034
-name: mangrove tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004035
-name: litchi tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004036
-name: laurel tree
-synonym: "Lauraceae tree" EXACT []
-synonym: "lauraceous tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004037
-name: Larix sibirica tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004038
-name: larch tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004039
-name: kraft pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004040
-name: Korean native pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004041
-name: Korean lacquer tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004042
-name: Korean fir tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004043
-name: Korea spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004044
-name: kiwifruit tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004045
-name: khat tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004046
-name: jujube tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004047
-name: Juglandaceae walnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004048
-name: Japanese Yew tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004049
-name: Japanese larch tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004050
-name: jack pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004051
-name: Indian yew tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004052
-name: Indian oak tree
-is_a: OBT:001666 ! oak
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004053
-name: Indian cork tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004054
-name: Iberian oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004055
-name: holm oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004056
-name: Himalayan pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004057
-name: hazelnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004058
-name: guava tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004059
-name: grapefruit tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004060
-name: Garry oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004061
-name: Garcinia schomdurgkiana Pierre tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004062
-name: evergreen oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004063
-name: European white elm
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004064
-name: European hackberry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004065
-name: European elm
-is_a: OBT:001542 ! elm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004066
-name: eucalyptus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004067
-name: English oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004068
-name: Engelmann spruce
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004069
-name: Emory oak
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004070
-name: Eastern cottonwood tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004071
-name: Dutch elm
-is_a: OBT:001542 ! elm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004072
-name: deciduous tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004073
-name: cypress tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004074
-name: cotton tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004075
-name: Azerbaijani almond tree
-is_a: OBT:001402 ! almond tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004076
-name: coffee tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004077
-name: coconut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004078
-name: cocoa tree
-synonym: "chocolate tree" EXACT []
-synonym: "Theobroma cacao" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004079
-name: clove tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004080
-name: clementine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004081
-name: chestnut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004082
-name: Cherry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004083
-name: carob tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004084
-name: camellia tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004085
-name: brazil nut tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004086
-name: blueberry tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004087
-name: black oak tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004088
-name: Bishop pine
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004090
-name: Betula tree
-synonym: "Betulaceae tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004091
-name: Betula pendula tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004092
-name: beech tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004093
-name: banyan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004094
-name: avocado tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004095
-name: Austrian pine
-synonym: "Austrian pine tree" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004096
-name: Australian native pine tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004097
-name: Australian native Grey Box tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004098
-name: Australian Hibiscus tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004099
-name: Aspen tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004100
-name: argan tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004101
-name: Alep pine
-is_a: OBT:002187 ! pine
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004102
-name: ald tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004103
-name: acerola tree
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004104
-name: acacia tree
-synonym: "acacia" EXACT []
-is_a: OBT:001360 ! tree
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T13:37:57Z
-
-[Term]
-id: OBT:004106
-name: orchad
-is_a: OBT:000067 ! cultivated habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004107
-name: planthopper
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004108
-name: jumping plant lice
-synonym: "Psyllidae" NARROW []
-synonym: "psyllids" NARROW []
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004109
-name: sap-feeding insect
-synonym: "sap-sucking insect" NARROW []
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004110
-name: sentinel plant
-is_a: OBT:000912 ! terrestrial plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004111
-name: peony
-is_a: OBT:004110 ! sentinel plant
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004112
-name: piercing-sucking insect
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004113
-name: Myzus persicae
-synonym: "green peach aphid" EXACT []
-is_a: OBT:001428 ! aphid
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004114
-name: cabbage aphid
-synonym: "Brevicoryne brassicae" EXACT []
-is_a: OBT:001428 ! aphid
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004115
-name: phytophagous insect
-is_a: OBT:001163 ! insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004116
-name: cotton boll worm
-synonym: "Helicoverpa armigera" EXACT []
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004117
-name: black cut worm
-synonym: "Agrotis ipsilon" EXACT []
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004118
-name: cotton leaf worm
-is_a: OBT:001385 ! worm
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004119
-name: rice yellow stem borer
-synonym: "Scirpophaga incertulas" EXACT []
-is_a: OBT:001652 ! moth
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004120
-name: Asian citrus psyllid
-synonym: "Diaphorina citri" EXACT []
-is_a: OBT:004108 ! jumping plant lice
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004121
-name: vineyard
-is_a: OBT:000067 ! cultivated habitat
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004122
-name: Graphocephala versuta
-is_a: OBT:002248 ! sharpshooter
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:004123
-name: xylem sap-feeding insect
-is_a: OBT:004109 ! sap-feeding insect
-created_by: Claire_Nedellec
-creation_date: 2021-02-18T17:35:57Z
-
-[Term]
-id: OBT:009115
-name: palm forest
-is_a: OBT:003864 ! forest of given species
-created_by: Claire_Nedellec
-creation_date: 2021-02-16T17:38:57Z
-
-- 
GitLab


From b571b784a32d06034ade30b79573b9accd183477 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Fri, 5 Mar 2021 09:04:22 +0000
Subject: [PATCH 64/64] Update generate_stats.snakefile

---
 generate_stats.snakefile | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 0f3be205..8504c5d3 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -1,3 +1,5 @@
+#localrules: stats_cirm_BIA
+
 '''
 all
 '''
@@ -19,7 +21,7 @@ rule stats_cirm_BIA:
 	input:
 		file="corpora/cirm/{file}"
 	output:
-		stats="corpora/cirm/stats/{file}_stats.csv"
+		stats="corpora/cirm/stats/{file,.*xlsx}_stats.csv"
 	params:
 		result="cirm/{file}",
 		c0="source",
@@ -29,7 +31,7 @@ rule stats_cirm_BIA:
 		c="line"
 	run:
 		import pandas
-		df1 = pandas.read_excel(input.file, names = [params.c], header=None)
+		df1 = pandas.read_excel(input.file)
 		df2 = pandas.DataFrame({params.c0: params.v0, params.c1: [params.result], params.c2: [len(df1.index)]})
 		df2.to_csv(output.stats, index=False)
 
@@ -46,7 +48,7 @@ rule stats_cirm_Levure:
 	input:
 		file="corpora/cirm/{file}"
 	output:
-		stats="corpora/cirm/stats/{file}_stats.csv"
+		stats="corpora/cirm/stats/{file,.*txt}_stats.csv"
 	params:
 		result="cirm/{file}",
 		c0="source",
@@ -81,7 +83,7 @@ genbank | nb entrees | count_lines(corpora/genbank/corpora/genbank/GenBank_extra
 genbank | nb entites | count_lines(corpora/genbank/mapped_taxids.txt)
 genbank | nb habitats | count_lines(corpora/genbank/mapped_habitats.txt)
 '''
-ENTREES_GENBANK = ["corpora/genbank/GenBank_extraction_20210127.tsv"]
+ENTREES_GENBANK = ["GenBank_extraction_20210127.tsv"]
 SORTIES_GENBANK = ["mapped_taxids.txt", "mapped_habitats.txt" ]
 FILES_GENBANK = ENTREES_GENBANK + SORTIES_GENBANK
 '''
@@ -284,10 +286,11 @@ rule stats_eval_BB19_rel:
 		c="line"
 	run:
 		import pandas
-		s = get_score_stats(input.file, "Standard scoring")
+		#s = get_score_stats(input.file, "Standard scoring")
 		l = get_score_stats(input.file, "Lives_In")
 		e = get_score_stats(input.file, "Exhibits")
-		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
+		#df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Standard_scoring", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], s['value'], l['value'], e['value']]})
+		df2 = pandas.DataFrame({params.c0: [params.v0, params.v0, params.v0], params.c1: [params.result+"#Mesure", params.result+"#Lives_In", params.result+"#Exhibits"], params.c2: [l['name'], l['value'], e['value']]})
 		df2.to_csv(output.stats, index=False)
 
 
-- 
GitLab