diff --git a/README.md b/README.md
index 8b60406dad99444462646fe57f69cac4a038d4b3..1f8fec2a648752b133cea33d647b5c2707873bde 100644
--- a/README.md
+++ b/README.md
@@ -63,7 +63,7 @@ The workflow relies on the following `structure of folders` to manage the resour
The main directories/files are:
* `plans/` contains the AlvisNLP plans that are text mining pipelines to extract the informations
* `corpora/` contains the textual data to process
-* `ancillaries/` contains ancillary data like ontologies, lexical data, grammars, language models
+* `share/` contains ancillary data like ontologies, lexical data, grammars, language models
* `softwares/` contains additional scripts, envs and config files
* `*.snakefile` are the snakemake pipelines which represent the execution entry points
diff --git a/all-bis.snakefile b/all-bis.snakefile
index c6b466b92d03f5f3abb78f68c823308ff81dfad8..1ca1244af71dd34062a65297493f488cd81ba2ee 100644
--- a/all-bis.snakefile
+++ b/all-bis.snakefile
@@ -8,34 +8,34 @@ rule all:
cirm_yeast='corpora/cirm/test-yeast.txt',
genbank='corpora/genbank/test-3.2.txt',
dsmz='corpora/dsmz/test-3.3.txt',
- microbes_habitat='ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt',
- microbes_phenotype='ancillaries/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt',
+ microbes_habitat='share/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt',
+ microbes_phenotype='share/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt',
index_folder='corpora/pubmed/index',
expander_folder='corpora/pubmed/expander'
- #onto_habitat_json='ancillaries/BioNLP-OST+EnovFood-Habitat.json',
- #onto_phenotype_json='ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
- #onto_use_json='ancillaries/BioNLP-OST+EnovFood-Use.json'
+ #onto_habitat_json='share/BioNLP-OST+EnovFood-Habitat.json',
+ #onto_phenotype_json='share/BioNLP-OST+EnovFood-Phenotype.json',
+ #onto_use_json='share/BioNLP-OST+EnovFood-Use.json'
rule preprocess_ontology:
input:
- ontobiotope='ancillaries/BioNLP-OST+EnovFood.obo',
- use_onto='ancillaries/BioNLP-OST+EnovFood-Use.obo',
- names='ancillaries/extended-microorganisms-taxonomy/names.dmp'
+ ontobiotope='share/BioNLP-OST+EnovFood.obo',
+ use_onto='share/BioNLP-OST+EnovFood-Use.obo',
+ names='share/extended-microorganisms-taxonomy/names.dmp'
output:
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.json',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
- 'ancillaries/BioNLP-OST+EnovFood-Use.json',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- #'ancillaries/BioNLP-OST+EnovFood-Use.tomap',
- 'ancillaries/food-process-lexicon.txt',
- 'ancillaries/NCBI_taxa_ontobiotope.txt',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- 'ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ 'share/BioNLP-OST+EnovFood-Habitat.json',
+ 'share/BioNLP-OST+EnovFood-Phenotype.json',
+ 'share/BioNLP-OST+EnovFood-Use.json',
+ 'share/BioNLP-OST+EnovFood-Habitat.tomap',
+ 'share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ #'share/BioNLP-OST+EnovFood-Use.tomap',
+ 'share/food-process-lexicon.txt',
+ 'share/NCBI_taxa_ontobiotope.txt',
+ 'share/BioNLP-OST+EnovFood-Habitat.obo',
+ 'share/BioNLP-OST+EnovFood-Phenotype.obo',
+ 'share/BioNLP-OST+EnovFood-Phenotype.paths',
+ 'share/BioNLP-OST+EnovFood-Habitat.paths',
+ 'share/BioNLP-OST+EnovFood-Use.paths'
shell: """snakemake --verbose \
--printshellcmds \
--use-singularity \
@@ -52,10 +52,10 @@ rule preprocess_ontology:
rule process_cirm_corpus:
input:
cirm_data='corpora/cirm/2019-07-05/extraction_3-fv.csv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
output:
'corpora/cirm/test.txt',
'corpora/cirm/test-yeast.txt'
@@ -73,11 +73,11 @@ rule process_cirm_corpus:
rule process_genbank_corpus:
input:
genbank_data='corpora/genbank/req1_sup800_bacteria-descriptors.csv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
'corpora/genbank/test-3.2.txt'
shell: """snakemake --verbose \
@@ -95,11 +95,11 @@ rule process_dsmz_corpus:
input:
dsmz_data1='corpora/dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv',
dsmz_data2='corpora/dsmz/dsmz-data/category=origin-key=sample_type.tsv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
'corpora/dsmz/test-3.3.txt'
shell: """snakemake --verbose \
@@ -118,16 +118,16 @@ BATCHES, = glob_wildcards("corpora/pubmed/batches/{id}/batch.xml")
rule process_pubmed_corpus:
input:
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
expander_folder=directory("corpora/pubmed/expander"),
index_folder=directory("corpora/pubmed/index"),
- florilege_Habitat_result="ancillaries/2019-12-12/PubMed-Habitat-2019-12-12.txt",
- florilege_Phenotype_result="ancillaries/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
+ florilege_Habitat_result="share/2019-12-12/PubMed-Habitat-2019-12-12.txt",
+ florilege_Phenotype_result="share/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
shell: """snakemake --verbose \
--printshellcmds \
--use-singularity \
diff --git a/all.snakefile b/all.snakefile
index e71e9497273339dc31f6d5d2603fa77e109122c2..1c84d19aad2ee63d9f12386f89eb6e253a47c35b 100644
--- a/all.snakefile
+++ b/all.snakefile
@@ -8,33 +8,33 @@ rule all:
cirm_yeast='corpora/cirm/test-yeast.txt',
genbank='corpora/genbank/test-3.2.txt',
dsmz='corpora/dsmz/test-3.3.txt',
- microbes_habitat='ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt',
- microbes_phenotype='ancillaries/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt',
+ microbes_habitat='share/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt',
+ microbes_phenotype='share/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt',
index_folder='corpora/pubmed/index',
expander_folder='corpora/pubmed/expander'
- #onto_habitat_json='ancillaries/BioNLP-OST+EnovFood-Habitat.json',
- #onto_phenotype_json='ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
- #onto_use_json='ancillaries/BioNLP-OST+EnovFood-Use.json'
+ #onto_habitat_json='share/BioNLP-OST+EnovFood-Habitat.json',
+ #onto_phenotype_json='share/BioNLP-OST+EnovFood-Phenotype.json',
+ #onto_use_json='share/BioNLP-OST+EnovFood-Use.json'
rule preprocess_ontology:
input:
- ontobiotope='ancillaries/BioNLP-OST+EnovFood.obo',
- use_onto='ancillaries/BioNLP-OST+EnovFood-Use.obo',
- names='ancillaries/extended-microorganisms-taxonomy/names.dmp'
+ ontobiotope='share/BioNLP-OST+EnovFood.obo',
+ use_onto='share/BioNLP-OST+EnovFood-Use.obo',
+ names='share/extended-microorganisms-taxonomy/names.dmp'
output:
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
- 'ancillaries/BioNLP-OST+EnovFood-Use.json',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- #'ancillaries/BioNLP-OST+EnovFood-Use.tomap',
- 'ancillaries/food-process-lexicon.txt',
- 'ancillaries/NCBI_taxa_ontobiotope.txt',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- 'ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ 'share/BioNLP-OST+EnovFood-Phenotype.json',
+ 'share/BioNLP-OST+EnovFood-Use.json',
+ 'share/BioNLP-OST+EnovFood-Habitat.tomap',
+ 'share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ #'share/BioNLP-OST+EnovFood-Use.tomap',
+ 'share/food-process-lexicon.txt',
+ 'share/NCBI_taxa_ontobiotope.txt',
+ 'share/BioNLP-OST+EnovFood-Habitat.obo',
+ 'share/BioNLP-OST+EnovFood-Phenotype.obo',
+ 'share/BioNLP-OST+EnovFood-Phenotype.paths',
+ 'share/BioNLP-OST+EnovFood-Habitat.paths',
+ 'share/BioNLP-OST+EnovFood-Use.paths'
shell: """snakemake --verbose \
--printshellcmds \
--use-singularity \
@@ -52,10 +52,10 @@ rule preprocess_ontology:
rule process_cirm_corpus:
input:
cirm_data='corpora/cirm/2019-07-05/extraction_3-fv.csv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
output:
'corpora/cirm/test.txt',
'corpora/cirm/test-yeast.txt'
@@ -75,11 +75,11 @@ rule process_cirm_corpus:
rule process_genbank_corpus:
input:
genbank_data='corpora/genbank/req1_sup800_bacteria-descriptors.csv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
'corpora/genbank/test-3.2.txt'
shell: """snakemake --verbose \
@@ -99,11 +99,11 @@ rule process_dsmz_corpus:
input:
dsmz_data1='corpora/dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv',
dsmz_data2='corpora/dsmz/dsmz-data/category=origin-key=sample_type.tsv',
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
'corpora/dsmz/test-3.3.txt'
shell: """snakemake --verbose \
@@ -124,16 +124,16 @@ BATCHES, = glob_wildcards("corpora/pubmed/batches/{id}/batch.xml")
rule process_pubmed_corpus:
input:
- habitat_tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- phenotype_tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- habitat_paths='ancillaries/BioNLP-OST+EnovFood-Habitat.paths',
- phenotype_paths='ancillaries/BioNLP-OST+EnovFood-Phenotype.paths',
- use_paths='ancillaries/BioNLP-OST+EnovFood-Use.paths'
+ habitat_tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ phenotype_tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ habitat_paths='share/BioNLP-OST+EnovFood-Habitat.paths',
+ phenotype_paths='share/BioNLP-OST+EnovFood-Phenotype.paths',
+ use_paths='share/BioNLP-OST+EnovFood-Use.paths'
output:
expander_folder=directory("corpora/pubmed/expander"),
index_folder=directory("corpora/pubmed/index"),
- florilege_Habitat_result="ancillaries/2019-12-12/PubMed-Habitat-2019-12-12.txt",
- florilege_Phenotype_result="ancillaries/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
+ florilege_Habitat_result="share/2019-12-12/PubMed-Habitat-2019-12-12.txt",
+ florilege_Phenotype_result="share/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
shell: """snakemake --verbose \
--printshellcmds \
--use-singularity \
diff --git a/config/config.yaml b/config/config.yaml
index 4c690578d68b3bf5aa6ba124c3add6a73b523540..294faf6ce56e1c049a63aae55f71434ab92cfe1e 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -4,21 +4,21 @@
TMP: "/tmp/"
# ontobiotope
-ONTOBIOTOPE: "ancillaries/BioNLP-OST+EnovFood.obo"
+ONTOBIOTOPE: "share/BioNLP-OST+EnovFood.obo"
HABITAT_ROOT: "OBT:000001"
PHENOTYPE_ROOT: "OBT:000002"
USE_ROOT: "OBT:004185"
-ONTOBIOTOPE_HABITAT: "ancillaries/BioNLP-OST+EnovFood-Habitat.obo"
-ONTOBIOTOPE_PHENOTYPE: "ancillaries/BioNLP-OST+EnovFood-Phenotype.obo"
-ONTOBIOTOPE_USE: "ancillaries/BioNLP-OST+EnovFood-Use.obo"
+ONTOBIOTOPE_HABITAT: "share/BioNLP-OST+EnovFood-Habitat.obo"
+ONTOBIOTOPE_PHENOTYPE: "share/BioNLP-OST+EnovFood-Phenotype.obo"
+ONTOBIOTOPE_USE: "share/BioNLP-OST+EnovFood-Use.obo"
# ncbi taxo
-NCBI_TAXO_ID: "ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt"
-NCBI_TAXO_MICROORGANISMS: "ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt"
-NCBI_TAXO_AND_ID_MICROORGANISMS: "ancillaries/extended-microorganisms-taxonomy/taxa+id_microorganisms.txt"
-NCBI_TAXO_NAMES: "ancillaries/extended-microorganisms-taxonomy/names.dmp"
-MAP_BACDIVE_TAXID: "ancillaries/extended-microorganisms-taxonomy/bacdive-to-taxid.txt"
-BACDIVE_ENTRIES: "ancillaries/extended-microorganisms-taxonomy/bacdive-strains/entries"
+NCBI_TAXO_ID: "share/extended-microorganisms-taxonomy/taxa+id_full.txt"
+NCBI_TAXO_MICROORGANISMS: "share/extended-microorganisms-taxonomy/taxid_microorganisms.txt"
+NCBI_TAXO_AND_ID_MICROORGANISMS: "share/extended-microorganisms-taxonomy/taxa+id_microorganisms.txt"
+NCBI_TAXO_NAMES: "share/extended-microorganisms-taxonomy/names.dmp"
+MAP_BACDIVE_TAXID: "share/extended-microorganisms-taxonomy/bacdive-to-taxid.txt"
+BACDIVE_ENTRIES: "share/extended-microorganisms-taxonomy/bacdive-strains/entries"
## cirm
@@ -58,12 +58,16 @@ DSMZ_RESULT: "corpora/dsmz/test-3.3.txt"
PUBMED_FOLDER_NAME: "pubmed"
PUBMED_CORPUS_HOME: "corpora/pubmed"
PUBMED_BATCHES_HOME: "corpora/pubmed/batches"
-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"
+PUBMED_HABITAT_RESULT: "share/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt"
+PUBMED_PHENOTYPE_RESULT: "share/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt"
PUBMED_DB: "/db/pubmed/current/index"
PUBMED_MICROBIO_MESH_TERMS: "corpora/pubmed/microbio-mesh-terms.txt"
PUBMED_XSLT_FILE: "corpora/pubmed/microbes-2019-pubmed2alvisnlp.xslt"
+## epmc
+PMC_REQUEST_ROOT: "https://www.ebi.ac.uk/europepmc/webservices/rest/"
+
+
## bionlp-ost
BIONLPOST_BATCHES_HOME: "corpora/BioNLP-OST-2019/batches"
BIONLPOST_API: "http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/api"
@@ -71,7 +75,7 @@ BIONLPOST_API: "http://bibliome.jouy.inra.fr/demo/BioNLP-OST-2019-Evaluation/api
## index
ALVISIR_INDEX: "corpora/pubmed/index"
ALVISIR_EXPANDER: "corpora/pubmed/expander"
-ALVISIR_EXPANDER_CONF: "ancillaries/expander.xml"
+ALVISIR_EXPANDER_CONF: "share/expander.xml"
## alvisnlp singlarity image
SINGULARITY_IMG: "softwares/alvisnlp.sif"
@@ -90,7 +94,7 @@ PLAN_FOLDER: "plans/"
SOFT_FOLDER: "softwares/"
-ANCI_FOLDER: "ancillaries/"
+ANCI_FOLDER: "share/"
## full entity results folder
diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json
index 77204d1ca1ee0328b760127ea8ce76ae04de9627..2411d3beeca4074be019316c3816759119fd49eb 100644
--- a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json
+++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json
@@ -1,6 +1,6 @@
{
"evaluation": {
- "submission-id": 707,
+ "submission-id": 711,
"global-evaluations": [{
"name": "Standard pairing",
"scorings": [{
@@ -8,21 +8,27 @@
"measures": [
{
"name": "mean-references",
- "value": 0.31154308415369136
+ "value": 0.3107107394196726
},
{
"name": "Predictions",
- "value": 468
+ "value": 417
},
{
"name": "False Negatives",
- "value": 301
+ "value": 305
}
]
}]
}]
},
"messages": [
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-14657131.a2",
+ "lineno": 20,
+ "level": "SERIOUS",
+ "body": "referent 3107983 is not in the vocabulary"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-14657131.a2",
"lineno": 26,
@@ -43,141 +49,165 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2",
- "lineno": 14,
+ "lineno": 16,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2",
- "lineno": 15,
+ "lineno": 17,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2",
- "lineno": 16,
+ "lineno": 18,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-21511409.a2",
- "lineno": 39,
+ "lineno": 36,
"level": "SERIOUS",
"body": "referent OBT:003719 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2",
- "lineno": 40,
+ "lineno": 38,
"level": "SERIOUS",
"body": "referent bd:133442 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2",
- "lineno": 45,
+ "lineno": 43,
"level": "SERIOUS",
"body": "referent bd:134026 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2",
- "lineno": 46,
+ "lineno": 44,
"level": "SERIOUS",
"body": "referent bd:134026 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2",
- "lineno": 47,
+ "lineno": 45,
"level": "SERIOUS",
"body": "referent bd:134026 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 36,
+ "lineno": 34,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 37,
+ "lineno": 35,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 41,
+ "lineno": 39,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 43,
+ "lineno": 41,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 44,
+ "lineno": 42,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 45,
+ "lineno": 43,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 46,
+ "lineno": 44,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 47,
+ "lineno": 45,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 48,
+ "lineno": 46,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 49,
+ "lineno": 47,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25644009.a2",
- "lineno": 50,
+ "lineno": 48,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-2617654.a2",
- "lineno": 37,
+ "lineno": 31,
"level": "SERIOUS",
"body": "referent OBT:004147 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-2617654.a2",
- "lineno": 38,
+ "lineno": 32,
"level": "SERIOUS",
"body": "referent OBT:003836 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2",
- "lineno": 65,
+ "lineno": 50,
+ "level": "SERIOUS",
+ "body": "referent OBT:004191 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2",
+ "lineno": 59,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2",
- "lineno": 67,
+ "lineno": 61,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-17953562-001.a2",
+ "lineno": 62,
+ "level": "SERIOUS",
+ "body": "referent 2816326 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-24010601-011.a2",
+ "lineno": 30,
+ "level": "SERIOUS",
+ "body": "referent OBT:004203 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-25955289-003.a2",
+ "lineno": 15,
+ "level": "SERIOUS",
+ "body": "referent OBT:004138 is not in the vocabulary"
}
],
"highest-message-level": "SERIOUS",
diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
index 5a4cd0181e2dfe65961fcf6a14afe578d359ad40..f2f8d27907e01edbeccfab79e7c3f12b95587cb2 100644
--- a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
+++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json
@@ -1,6 +1,6 @@
{
"evaluation": {
- "submission-id": 708,
+ "submission-id": 710,
"global-evaluations": [
{
"name": "Standard pairing",
@@ -10,39 +10,39 @@
"measures": [
{
"name": "SER",
- "value": 0.675531914893617
+ "value": 0.6409574468085106
},
{
"name": "ISER",
- "value": 0.5968253968253968
+ "value": 0.6094003241491086
},
{
"name": "Mismatches",
- "value": 221.98219518468412
+ "value": 207.47297916040836
},
{
"name": "Matches",
- "value": 970.0178048153165
+ "value": 963.5270208395923
},
{
"name": "Insertions",
- "value": 361
+ "value": 289
},
{
"name": "Deletions",
- "value": 688
+ "value": 709
},
{
"name": "Recall",
- "value": 0.5159669174549556
+ "value": 0.5125143727870172
},
{
"name": "Precision",
- "value": 0.6246090179106996
+ "value": 0.6599500142736934
},
{
"name": "Predictions",
- "value": 1553
+ "value": 1460
}
]
},
@@ -51,39 +51,39 @@
"measures": [
{
"name": "SER",
- "value": 0.7295081967213115
+ "value": 0.6487119437939111
},
{
"name": "ISER",
- "value": 0.5781990521327014
+ "value": 0.6065340909090909
},
{
"name": "Mismatches",
- "value": 198.2192053736142
+ "value": 183.45998934933837
},
{
"name": "Matches",
- "value": 449.7807946263862
+ "value": 443.5400106506622
},
{
"name": "Insertions",
- "value": 219
+ "value": 144
},
{
"name": "Deletions",
- "value": 206
+ "value": 227
},
{
"name": "Recall",
- "value": 0.5266754035437777
+ "value": 0.5193676939703304
},
{
"name": "Precision",
- "value": 0.5187783098343555
+ "value": 0.5752788724392506
},
{
"name": "Predictions",
- "value": 867
+ "value": 771
}
]
},
@@ -92,39 +92,39 @@
"measures": [
{
"name": "SER",
- "value": 0.8290398126463701
+ "value": 0.7447306791569087
},
{
"name": "ISER",
- "value": 0.5467349551856594
+ "value": 0.5731543624161074
},
{
"name": "Mismatches",
- "value": 283.55593636297465
+ "value": 265.8678411248794
},
{
"name": "Matches",
- "value": 364.4440636370252
+ "value": 361.1321588751204
},
{
"name": "Insertions",
- "value": 219
+ "value": 144
},
{
"name": "Deletions",
- "value": 206
+ "value": 227
},
{
"name": "Recall",
- "value": 0.42674948903632925
+ "value": 0.4228713804158319
},
{
"name": "Precision",
- "value": 0.42035070777050193
+ "value": 0.46839449918952064
},
{
"name": "Predictions",
- "value": 867
+ "value": 771
}
]
},
@@ -133,15 +133,15 @@
"measures": [
{
"name": "SER",
- "value": 1.355263157894737
+ "value": 0.8461538461538461
},
{
"name": "ISER",
- "value": 0.4245810055865921
+ "value": 0.5416666666666666
},
{
"name": "Mismatches",
- "value": 52.36475179550699
+ "value": 41.36475179550699
},
{
"name": "Matches",
@@ -149,7 +149,7 @@
},
{
"name": "Insertions",
- "value": 41
+ "value": 4
},
{
"name": "Deletions",
@@ -157,15 +157,15 @@
},
{
"name": "Recall",
- "value": 0.17941116058543433
+ "value": 0.20977304929989243
},
{
"name": "Precision",
- "value": 0.12743222621021502
+ "value": 0.23110590177106793
},
{
"name": "Predictions",
- "value": 107
+ "value": 59
}
]
},
@@ -182,31 +182,31 @@
},
{
"name": "Mismatches",
- "value": 97.2604323172907
+ "value": 91.2604323172907
},
{
"name": "Matches",
- "value": 59.73956768270931
+ "value": 60.73956768270931
},
{
"name": "Insertions",
- "value": 8
+ "value": 9
},
{
"name": "Deletions",
- "value": 58
+ "value": 63
},
{
"name": "Recall",
- "value": 0.27785845433818285
+ "value": 0.2825096171288805
},
{
"name": "Precision",
- "value": 0.36205798595581395
+ "value": 0.3772643955447783
},
{
"name": "Predictions",
- "value": 165
+ "value": 161
}
]
},
@@ -215,23 +215,23 @@
"measures": [
{
"name": "SER",
- "value": 0.825
+ "value": 0.834375
},
{
"name": "ISER",
- "value": 0.547945205479452
+ "value": 0.545144804088586
},
{
"name": "Mismatches",
- "value": 9.99749951153148
+ "value": 10.24749951153148
},
{
"name": "Matches",
- "value": 63.0025004884685
+ "value": 62.7525004884685
},
{
"name": "Insertions",
- "value": 8
+ "value": 10
},
{
"name": "Deletions",
@@ -239,15 +239,15 @@
},
{
"name": "Recall",
- "value": 0.19688281402646407
+ "value": 0.19610156402646406
},
{
"name": "Precision",
- "value": 0.777808648005784
+ "value": 0.7560542227526326
},
{
"name": "Predictions",
- "value": 81
+ "value": 83
}
]
},
@@ -256,23 +256,23 @@
"measures": [
{
"name": "SER",
- "value": 0.853125
+ "value": 0.8625
},
{
"name": "ISER",
- "value": 0.5396290050590219
+ "value": 0.5369127516778524
},
{
"name": "Mismatches",
- "value": 18.776938747526984
+ "value": 19.026938747526984
},
{
"name": "Matches",
- "value": 54.223061252473016
+ "value": 53.973061252473016
},
{
"name": "Insertions",
- "value": 8
+ "value": 10
},
{
"name": "Deletions",
@@ -280,15 +280,15 @@
},
{
"name": "Recall",
- "value": 0.16944706641397816
+ "value": 0.16866581641397818
},
{
"name": "Precision",
- "value": 0.6694205092897904
+ "value": 0.6502778464153376
},
{
"name": "Predictions",
- "value": 81
+ "value": 83
}
]
},
@@ -350,7 +350,7 @@
},
{
"name": "Matches",
- "value": 21.000000000000004
+ "value": 21
},
{
"name": "Insertions",
@@ -362,11 +362,11 @@
},
{
"name": "Recall",
- "value": 0.2470588235294118
+ "value": 0.24705882352941178
},
{
"name": "Precision",
- "value": 0.7241379310344829
+ "value": 0.7241379310344828
},
{
"name": "Predictions",
@@ -379,39 +379,39 @@
"measures": [
{
"name": "SER",
- "value": 0.7563884156729132
+ "value": 0.6993185689948893
},
{
"name": "ISER",
- "value": 0.5693501454898157
+ "value": 0.5884711779448621
},
{
"name": "Mismatches",
- "value": 208.21670488514562
+ "value": 193.7074888608698
},
{
"name": "Matches",
- "value": 512.7832951148544
+ "value": 506.29251113913034
},
{
"name": "Insertions",
- "value": 227
+ "value": 154
},
{
"name": "Deletions",
- "value": 453
+ "value": 474
},
{
"name": "Recall",
- "value": 0.4367830452426357
+ "value": 0.4312542684319679
},
{
"name": "Precision",
- "value": 0.5409106488553316
+ "value": 0.5928483736992158
},
{
"name": "Predictions",
- "value": 948
+ "value": 854
}
]
},
@@ -420,39 +420,39 @@
"measures": [
{
"name": "SER",
- "value": 0.8364565587734242
+ "value": 0.7768313458262351
},
{
"name": "ISER",
- "value": 0.5445269016697588
+ "value": 0.5627996164908916
},
{
"name": "Mismatches",
- "value": 302.33287511050156
+ "value": 284.8947798724064
},
{
"name": "Matches",
- "value": 418.6671248894982
+ "value": 415.1052201275934
},
{
"name": "Insertions",
- "value": 227
+ "value": 154
},
{
"name": "Deletions",
- "value": 453
+ "value": 474
},
{
"name": "Recall",
- "value": 0.3566159496503392
+ "value": 0.3535819592228223
},
{
"name": "Precision",
- "value": 0.4416319882800614
+ "value": 0.48607168633207654
},
{
"name": "Predictions",
- "value": 948
+ "value": 854
}
]
},
@@ -461,15 +461,15 @@
"measures": [
{
"name": "SER",
- "value": 1.231578947368421
+ "value": 0.8214285714285714
},
{
"name": "ISER",
- "value": 0.4481132075471698
+ "value": 0.5490196078431373
},
{
"name": "Mismatches",
- "value": 52.36475179550699
+ "value": 41.36475179550699
},
{
"name": "Matches",
@@ -477,7 +477,7 @@
},
{
"name": "Insertions",
- "value": 43
+ "value": 6
},
{
"name": "Deletions",
@@ -485,15 +485,15 @@
},
{
"name": "Recall",
- "value": 0.21721313899466327
+ "value": 0.24565771672015488
},
{
"name": "Precision",
- "value": 0.17789007072838803
+ "value": 0.30345953241901485
},
{
"name": "Predictions",
- "value": 116
+ "value": 68
}
]
},
@@ -510,31 +510,31 @@
},
{
"name": "Mismatches",
- "value": 103.2604323172907
+ "value": 97.2604323172907
},
{
"name": "Matches",
- "value": 80.7395676827093
+ "value": 81.7395676827093
},
{
"name": "Insertions",
- "value": 10
+ "value": 11
},
{
"name": "Deletions",
- "value": 116
+ "value": 121
},
{
"name": "Recall",
- "value": 0.26913189227569767
+ "value": 0.272465225609031
},
{
"name": "Precision",
- "value": 0.41618333857066653
+ "value": 0.43020825096162796
},
{
"name": "Predictions",
- "value": 194
+ "value": 190
}
]
},
@@ -543,11 +543,11 @@
"measures": [
{
"name": "SER",
- "value": 0.5410764872521246
+ "value": 0.5424929178470255
},
{
"name": "ISER",
- "value": 0.6488970588235293
+ "value": 0.6483011937557392
},
{
"name": "Mismatches",
@@ -559,7 +559,7 @@
},
{
"name": "Insertions",
- "value": 134
+ "value": 135
},
{
"name": "Deletions",
@@ -571,11 +571,11 @@
},
{
"name": "Precision",
- "value": 0.7557595201660521
+ "value": 0.754512392244986
},
{
"name": "Predictions",
- "value": 605
+ "value": 606
}
]
},
@@ -584,39 +584,39 @@
"measures": [
{
"name": "SER",
- "value": 0.6170212765957447
+ "value": 0.5856382978723405
},
{
"name": "ISER",
- "value": 0.6184210526315789
+ "value": 0.6306608520630661
},
{
"name": "Mismatches",
- "value": 111.768894894641
+ "value": 103.41862925245574
},
{
"name": "Matches",
- "value": 1080.2311051053591
+ "value": 1067.5813707475443
},
{
"name": "Insertions",
- "value": 361
+ "value": 289
},
{
"name": "Deletions",
- "value": 688
+ "value": 709
},
{
"name": "Recall",
- "value": 0.5745910133539144
+ "value": 0.5678624312486937
},
{
"name": "Precision",
- "value": 0.6955770155218024
+ "value": 0.7312201169503728
},
{
"name": "Predictions",
- "value": 1553
+ "value": 1460
}
]
},
@@ -625,39 +625,39 @@
"measures": [
{
"name": "SER",
- "value": 0.6229508196721312
+ "value": 0.5491803278688525
},
{
"name": "ISER",
- "value": 0.6161616161616161
+ "value": 0.6455026455026455
},
{
"name": "Mismatches",
- "value": 107.1865156874975
+ "value": 98.83625004531228
},
{
"name": "Matches",
- "value": 540.8134843125025
+ "value": 528.1637499546878
},
{
"name": "Insertions",
- "value": 219
+ "value": 144
},
{
"name": "Deletions",
- "value": 206
+ "value": 227
},
{
"name": "Recall",
- "value": 0.6332710589139373
+ "value": 0.6184587236003369
},
{
"name": "Precision",
- "value": 0.6237756451124596
+ "value": 0.6850372891759894
},
{
"name": "Predictions",
- "value": 867
+ "value": 771
}
]
},
@@ -666,39 +666,39 @@
"measures": [
{
"name": "SER",
- "value": 0.7704918032786885
+ "value": 0.689695550351288
},
{
"name": "ISER",
- "value": 0.5648148148148149
+ "value": 0.5918225918225918
},
{
"name": "Mismatches",
- "value": 233.53333333333305
+ "value": 218.53333333333308
},
{
"name": "Matches",
- "value": 414.46666666666613
+ "value": 408.46666666666613
},
{
"name": "Insertions",
- "value": 219
+ "value": 144
},
{
"name": "Deletions",
- "value": 206
+ "value": 227
},
{
"name": "Recall",
- "value": 0.4853239656518339
+ "value": 0.4782982045277121
},
{
"name": "Precision",
- "value": 0.4780469050365238
+ "value": 0.5297881539126669
},
{
"name": "Predictions",
- "value": 867
+ "value": 771
}
]
},
@@ -707,15 +707,15 @@
"measures": [
{
"name": "SER",
- "value": 0.809375
+ "value": 0.815625
},
{
"name": "ISER",
- "value": 0.5526770293609672
+ "value": 0.5507745266781411
},
{
"name": "Mismatches",
- "value": 4.58237920714345
+ "value": 4.582379207143451
},
{
"name": "Matches",
@@ -723,7 +723,7 @@
},
{
"name": "Insertions",
- "value": 8
+ "value": 10
},
{
"name": "Deletions",
@@ -735,11 +735,11 @@
},
{
"name": "Precision",
- "value": 0.8446619850969943
+ "value": 0.8243086842512836
},
{
"name": "Predictions",
- "value": 81
+ "value": 83
}
]
},
@@ -748,11 +748,11 @@
"measures": [
{
"name": "SER",
- "value": 0.84375
+ "value": 0.85
},
{
"name": "ISER",
- "value": 0.5423728813559322
+ "value": 0.5405405405405405
},
{
"name": "Mismatches",
@@ -764,7 +764,7 @@
},
{
"name": "Insertions",
- "value": 8
+ "value": 10
},
{
"name": "Deletions",
@@ -776,11 +776,11 @@
},
{
"name": "Precision",
- "value": 0.7160493827160493
+ "value": 0.6987951807228916
},
{
"name": "Predictions",
- "value": 81
+ "value": 83
}
]
},
@@ -789,39 +789,39 @@
"measures": [
{
"name": "SER",
- "value": 0.6737649063032368
+ "value": 0.6226575809199318
},
{
"name": "ISER",
- "value": 0.5974554707379135
+ "value": 0.6162729658792651
},
{
"name": "Mismatches",
- "value": 111.768894894641
+ "value": 103.41862925245574
},
{
"name": "Matches",
- "value": 609.2311051053584
+ "value": 596.5813707475439
},
{
"name": "Insertions",
- "value": 227
+ "value": 154
},
{
"name": "Deletions",
- "value": 453
+ "value": 474
},
{
"name": "Recall",
- "value": 0.5189362053708334
+ "value": 0.5081613038735467
},
{
"name": "Precision",
- "value": 0.6426488450478465
+ "value": 0.6985730336622294
},
{
"name": "Predictions",
- "value": 948
+ "value": 854
}
]
},
@@ -830,39 +830,39 @@
"measures": [
{
"name": "SER",
- "value": 0.7904599659284497
+ "value": 0.7333901192504259
},
{
"name": "ISER",
- "value": 0.5585156993339677
+ "value": 0.5769041769041768
},
{
"name": "Mismatches",
- "value": 248.53333333333305
+ "value": 233.53333333333305
},
{
"name": "Matches",
- "value": 472.4666666666661
+ "value": 466.466666666666
},
{
"name": "Insertions",
- "value": 227
+ "value": 154
},
{
"name": "Deletions",
- "value": 453
+ "value": 474
},
{
"name": "Recall",
- "value": 0.4024417944349796
+ "value": 0.3973310618966491
},
{
"name": "Precision",
- "value": 0.4983825597749642
+ "value": 0.5462138953942225
},
{
"name": "Predictions",
- "value": 948
+ "value": 854
}
]
},
@@ -871,11 +871,11 @@
"measures": [
{
"name": "SER",
- "value": 0.5226628895184136
+ "value": 0.5240793201133145
},
{
"name": "ISER",
- "value": 0.6567441860465116
+ "value": 0.6561338289962825
},
{
"name": "Mismatches",
@@ -887,7 +887,7 @@
},
{
"name": "Insertions",
- "value": 134
+ "value": 135
},
{
"name": "Deletions",
@@ -899,11 +899,11 @@
},
{
"name": "Precision",
- "value": 0.7785123966942149
+ "value": 0.7772277227722773
},
{
"name": "Predictions",
- "value": 605
+ "value": 606
}
]
},
@@ -1122,39 +1122,39 @@
"measures": [
{
"name": "SER",
- "value": 0.5345744680851063
+ "value": 0.5010638297872341
},
{
"name": "ISER",
- "value": 0.6516464471403813
+ "value": 0.666194188518781
},
{
"name": "Mismatches",
- "value": 158.4083979766892
+ "value": 144.57561649144267
},
{
"name": "Matches",
- "value": 1134.5916020233105
+ "value": 1126.4243835085574
},
{
"name": "Insertions",
- "value": 260
+ "value": 189
},
{
"name": "Deletions",
- "value": 587
+ "value": 609
},
{
"name": "Recall",
- "value": 0.603506171288995
+ "value": 0.599161906121573
},
{
"name": "Precision",
- "value": 0.7305805550697427
+ "value": 0.771523550348327
},
{
"name": "Predictions",
- "value": 1553
+ "value": 1460
}
]
},
@@ -1163,39 +1163,39 @@
"measures": [
{
"name": "SER",
- "value": 0.6242774566473989
+ "value": 0.5511627906976744
},
{
"name": "ISER",
- "value": 0.6156583629893239
+ "value": 0.6446776611694153
},
{
"name": "Mismatches",
- "value": 128.1421154515353
+ "value": 114.05933396628876
},
{
"name": "Matches",
- "value": 532.8578845484645
+ "value": 522.9406660337113
},
{
"name": "Insertions",
- "value": 208
+ "value": 137
},
{
"name": "Deletions",
- "value": 204
+ "value": 223
},
{
"name": "Recall",
- "value": 0.6160206757785717
+ "value": 0.6080705418996643
},
{
"name": "Precision",
- "value": 0.6131851375701548
+ "value": 0.6756339354440715
},
{
"name": "Predictions",
- "value": 869
+ "value": 774
}
]
},
@@ -1204,39 +1204,39 @@
"measures": [
{
"name": "SER",
- "value": 0.7839506172839507
+ "value": 0.7616099071207431
},
{
"name": "ISER",
- "value": 0.5605536332179931
+ "value": 0.5676625659050967
},
{
"name": "Mismatches",
- "value": 11.081289154846818
+ "value": 7.5142348912809265
},
{
"name": "Matches",
- "value": 76.91871084515319
+ "value": 84.4857651087191
},
{
"name": "Insertions",
- "value": 7
+ "value": 8
},
{
"name": "Deletions",
- "value": 236
+ "value": 231
},
{
"name": "Recall",
- "value": 0.23740342853442342
+ "value": 0.2615658362499043
},
{
"name": "Precision",
- "value": 0.8096706404752967
+ "value": 0.8448576510871909
},
{
"name": "Predictions",
- "value": 95
+ "value": 100
}
]
},
@@ -1245,39 +1245,39 @@
"measures": [
{
"name": "SER",
- "value": 0.6683587140439933
+ "value": 0.6096528365791702
},
{
"name": "ISER",
- "value": 0.5993914807302231
+ "value": 0.6212519726459758
},
{
"name": "Mismatches",
- "value": 135.40635034281624
+ "value": 121.57356885756968
},
{
"name": "Matches",
- "value": 606.5936496571836
+ "value": 605.4264311424303
},
{
"name": "Insertions",
- "value": 215
+ "value": 145
},
{
"name": "Deletions",
- "value": 440
+ "value": 454
},
{
"name": "Recall",
- "value": 0.5131925970026934
+ "value": 0.5126388070638698
},
{
"name": "Precision",
- "value": 0.6338491636961167
+ "value": 0.6942963659890256
},
{
"name": "Predictions",
- "value": 957
+ "value": 872
}
]
},
@@ -1286,35 +1286,35 @@
"measures": [
{
"name": "SER",
- "value": 0.3062937062937063
+ "value": 0.31215469613259667
},
{
"name": "ISER",
- "value": 0.765524625267666
+ "value": 0.7621052631578947
},
{
"name": "Mismatches",
- "value": 27.39157844619788
+ "value": 27.487166681492
},
{
"name": "Matches",
- "value": 540.608421553802
+ "value": 541.512833318508
},
{
"name": "Insertions",
- "value": 45
+ "value": 44
},
{
"name": "Deletions",
- "value": 147
+ "value": 155
},
{
"name": "Recall",
- "value": 0.756095694480842
+ "value": 0.7479459023736298
},
{
"name": "Precision",
- "value": 0.881906071050248
+ "value": 0.8833814572895726
},
{
"name": "Predictions",
@@ -1329,175 +1329,115 @@
"messages": [
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10618167.a2",
- "lineno": 11,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10618167.a2",
- "lineno": 12,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10645449.a2",
- "lineno": 19,
+ "lineno": 9,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10645449.a2",
- "lineno": 20,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 33,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 34,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 35,
+ "lineno": 9,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 36,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 37,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 38,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 39,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10665543.a2",
- "lineno": 40,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 47,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 48,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 49,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 50,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 51,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 52,
+ "lineno": 41,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 53,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 54,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 55,
+ "lineno": 44,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 56,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 57,
+ "lineno": 46,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 58,
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 59,
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 60,
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 61,
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 62,
+ "lineno": 51,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-10770276.a2",
- "lineno": 63,
+ "lineno": 52,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -1527,37 +1467,37 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 35,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 36,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 37,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 38,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 39,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12417169.a2",
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-11551069.a2",
- "lineno": 40,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12417169.a2",
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -1621,57 +1561,33 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12417169.a2",
- "lineno": 61,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12417169.a2",
- "lineno": 62,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12417169.a2",
- "lineno": 63,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 75,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 76,
+ "lineno": 65,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 77,
+ "lineno": 66,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 78,
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 79,
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-12438382.a2",
- "lineno": 80,
+ "lineno": 69,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -1695,15 +1611,15 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14638480.a2",
- "lineno": 11,
+ "lineno": 9,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14638480.a2",
- "lineno": 12,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14657131.a2",
+ "lineno": 20,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent 3107983 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14657131.a2",
@@ -1769,113 +1685,113 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14657131.a2",
"lineno": 36,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "unknown type: Exhibits"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-14657131.a2",
- "lineno": 37,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
+ "lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: Exhibits"
+ "body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 14,
+ "lineno": 17,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 15,
+ "lineno": 18,
"level": "SERIOUS",
"body": "referent bd:14460 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 16,
+ "lineno": 19,
"level": "SERIOUS",
- "body": "referent bd:14460 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 17,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 18,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 19,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 20,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 21,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 22,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 23,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15273106.a2",
- "lineno": 24,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 49,
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 50,
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 51,
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 52,
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 53,
+ "lineno": 51,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-15460321.a2",
- "lineno": 54,
+ "lineno": 52,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -1905,37 +1821,37 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 35,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 36,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 37,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 38,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 39,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-1649682.a2",
- "lineno": 40,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -2091,217 +2007,181 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-17261513.a2",
- "lineno": 19,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-17261513.a2",
- "lineno": 20,
+ "lineno": 11,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-17261513.a2",
- "lineno": 21,
+ "lineno": 12,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 49,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 50,
+ "lineno": 46,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 51,
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 52,
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 53,
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 54,
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 55,
+ "lineno": 51,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 56,
+ "lineno": 52,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 57,
+ "lineno": 53,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 58,
+ "lineno": 54,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 59,
+ "lineno": 55,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 60,
+ "lineno": 56,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 61,
+ "lineno": 57,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 62,
+ "lineno": 58,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 63,
+ "lineno": 59,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 64,
+ "lineno": 60,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 65,
+ "lineno": 61,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 66,
+ "lineno": 62,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 67,
+ "lineno": 63,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 68,
+ "lineno": 64,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 69,
+ "lineno": 65,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 70,
+ "lineno": 66,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 71,
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 72,
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19494280.a2",
- "lineno": 73,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 49,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 50,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 51,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 52,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 53,
+ "lineno": 69,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 54,
+ "lineno": 41,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 55,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-19656787.a2",
- "lineno": 56,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -2343,43 +2223,43 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 43,
+ "lineno": 39,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 44,
+ "lineno": 40,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 45,
+ "lineno": 41,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 46,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 47,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 48,
+ "lineno": 44,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-20672296.a2",
- "lineno": 49,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -2439,139 +2319,133 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21476570.a2",
- "lineno": 27,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21476570.a2",
- "lineno": 28,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21476570.a2",
- "lineno": 29,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21476570.a2",
- "lineno": 30,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 39,
+ "lineno": 36,
"level": "SERIOUS",
"body": "referent OBT:003719 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 65,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 66,
+ "lineno": 61,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 67,
+ "lineno": 62,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 68,
+ "lineno": 63,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 69,
+ "lineno": 64,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 70,
+ "lineno": 65,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 71,
+ "lineno": 66,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 72,
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 73,
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 74,
+ "lineno": 69,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21511409.a2",
- "lineno": 75,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 23,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 24,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 25,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 26,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
+ "lineno": 73,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 27,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
+ "lineno": 74,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 28,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
+ "lineno": 75,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-21989983.a2",
- "lineno": 29,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
+ "lineno": 76,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -2663,77 +2537,53 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
"lineno": 91,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
- "lineno": 92,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
- "lineno": 93,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
- "lineno": 94,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
- "lineno": 95,
- "level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22203552.a2",
- "lineno": 96,
+ "lineno": 92,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22537874.a2",
- "lineno": 19,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22537874.a2",
- "lineno": 20,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22537874.a2",
- "lineno": 21,
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-22537874.a2",
- "lineno": 22,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
+ "lineno": 38,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent bd:133442 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
- "lineno": 40,
+ "lineno": 43,
"level": "SERIOUS",
- "body": "referent bd:133442 is not in the vocabulary"
+ "body": "referent bd:134026 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
- "lineno": 45,
+ "lineno": 44,
"level": "SERIOUS",
"body": "referent bd:134026 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
- "lineno": 46,
+ "lineno": 45,
"level": "SERIOUS",
"body": "referent bd:134026 is not in the vocabulary"
},
@@ -2741,7 +2591,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
"lineno": 47,
"level": "SERIOUS",
- "body": "referent bd:134026 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
+ "lineno": 48,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
@@ -2783,19 +2639,43 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
"lineno": 55,
"level": "SERIOUS",
+ "body": "unknown type: Exhibits"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 49,
+ "level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
- "lineno": 56,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-23645023.a2",
- "lineno": 57,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 51,
"level": "SERIOUS",
- "body": "unknown type: Exhibits"
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 52,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 53,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
+ "lineno": 54,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
@@ -2876,134 +2756,50 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 68,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24739626.a2",
+ "lineno": 15,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 69,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24739626.a2",
+ "lineno": 16,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 70,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 71,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 72,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 73,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 74,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 75,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 76,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 77,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 78,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 79,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24389148.a2",
- "lineno": 80,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24739626.a2",
- "lineno": 15,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24739626.a2",
- "lineno": 16,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 39,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 40,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 41,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 42,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 43,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 44,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-24794581.a2",
- "lineno": 45,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -3027,196 +2823,136 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 71,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 72,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 73,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 74,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 75,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 76,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 77,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 78,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 79,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 80,
+ "lineno": 53,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 81,
+ "lineno": 54,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 82,
+ "lineno": 55,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 83,
+ "lineno": 56,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 84,
+ "lineno": 57,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 85,
+ "lineno": 58,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 86,
+ "lineno": 59,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 87,
+ "lineno": 60,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 88,
+ "lineno": 61,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 89,
+ "lineno": 62,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 90,
+ "lineno": 63,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 91,
+ "lineno": 64,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 92,
+ "lineno": 65,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 93,
+ "lineno": 66,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 94,
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 95,
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 96,
+ "lineno": 69,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 97,
+ "lineno": 70,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 98,
+ "lineno": 71,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 99,
+ "lineno": 72,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "unknown type: Exhibits"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 100,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25179651.a2",
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 101,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25179651.a2",
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25046729.a2",
- "lineno": 102,
- "level": "SERIOUS",
- "body": "unknown type: Exhibits"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25179651.a2",
"lineno": 69,
@@ -3350,38 +3086,38 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25179651.a2",
- "lineno": 91,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25607366.a2",
+ "lineno": 5,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25179651.a2",
- "lineno": 92,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
+ "lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent bd:166636 is not in the vocabulary"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25607366.a2",
- "lineno": 5,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
+ "lineno": 35,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 36,
+ "lineno": 39,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 37,
+ "lineno": 41,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 41,
+ "lineno": 42,
"level": "SERIOUS",
"body": "referent bd:166636 is not in the vocabulary"
},
@@ -3425,13 +3161,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
"lineno": 49,
"level": "SERIOUS",
- "body": "referent bd:166636 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
"lineno": 50,
"level": "SERIOUS",
- "body": "referent bd:166636 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
@@ -3469,195 +3205,111 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 57,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 58,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 59,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-25644009.a2",
- "lineno": 60,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-26155675.a2",
- "lineno": 21,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-26155675.a2",
- "lineno": 22,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 37,
+ "lineno": 31,
"level": "SERIOUS",
"body": "referent OBT:004147 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 38,
+ "lineno": 32,
"level": "SERIOUS",
"body": "referent OBT:003836 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 53,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 54,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 55,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 56,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 57,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 58,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
- "lineno": 59,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 43,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 44,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
"lineno": 45,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
"lineno": 46,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
"lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-2617654.a2",
"lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 49,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 50,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 51,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 52,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3015879.a2",
- "lineno": 53,
+ "lineno": 39,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 39,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 40,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 41,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 42,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 43,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-3516874.a2",
- "lineno": 44,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -3675,19 +3327,19 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-817056.a2",
- "lineno": 25,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-817056.a2",
- "lineno": 26,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-817056.a2",
- "lineno": 27,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -3717,244 +3369,202 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 61,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 62,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 63,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 64,
+ "lineno": 57,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 65,
+ "lineno": 58,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 66,
+ "lineno": 59,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 67,
+ "lineno": 60,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 68,
+ "lineno": 61,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 69,
+ "lineno": 62,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 70,
+ "lineno": 63,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 71,
+ "lineno": 64,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 72,
+ "lineno": 65,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 73,
+ "lineno": 66,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 74,
+ "lineno": 67,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 75,
+ "lineno": 68,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 76,
+ "lineno": 69,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 77,
+ "lineno": 70,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 78,
+ "lineno": 71,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 79,
+ "lineno": 72,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 80,
+ "lineno": 73,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-8698477.a2",
- "lineno": 81,
+ "lineno": 74,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 45,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 46,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 47,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 48,
+ "lineno": 41,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 49,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 50,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 51,
+ "lineno": 44,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 52,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 53,
+ "lineno": 46,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 54,
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 55,
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 56,
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 57,
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 58,
+ "lineno": 51,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "unknown type: Exhibits"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 59,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
+ "lineno": 85,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 60,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
+ "lineno": 86,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 61,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
+ "lineno": 87,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 62,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
+ "lineno": 88,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9231420.a2",
- "lineno": 63,
- "level": "SERIOUS",
- "body": "unknown type: Exhibits"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
"lineno": 89,
@@ -4130,40 +3740,58 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
- "lineno": 118,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 50,
+ "level": "SERIOUS",
+ "body": "referent OBT:004191 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 59,
+ "level": "SERIOUS",
+ "body": "referent bd:14460 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 61,
+ "level": "SERIOUS",
+ "body": "referent bd:14460 is not in the vocabulary"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 79,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
- "lineno": 119,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 80,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
- "lineno": 120,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 81,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9562874.a2",
- "lineno": 121,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
+ "lineno": 82,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 65,
+ "lineno": 83,
"level": "SERIOUS",
- "body": "referent bd:14460 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 67,
+ "lineno": 84,
"level": "SERIOUS",
- "body": "referent bd:14460 is not in the vocabulary"
+ "body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
@@ -4250,38 +3878,14 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 99,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 100,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 101,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 102,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 103,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9666962.a2",
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9575437.a2",
- "lineno": 104,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9666962.a2",
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -4339,24 +3943,6 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9666962.a2",
- "lineno": 58,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9666962.a2",
- "lineno": 59,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-9666962.a2",
- "lineno": 60,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-000.a2",
"lineno": 33,
@@ -4425,15 +4011,9 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-001.a2",
- "lineno": 69,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-001.a2",
- "lineno": 70,
+ "lineno": 62,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent 2816326 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-001.a2",
@@ -4555,12 +4135,30 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-001.a2",
+ "lineno": 91,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-002.a2",
"lineno": 21,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
+ "lineno": 23,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
+ "lineno": 24,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
"lineno": 25,
@@ -4697,62 +4295,38 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
"lineno": 47,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 48,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 49,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 50,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "unknown type: Exhibits"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 51,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
+ "lineno": 13,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 52,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
+ "lineno": 14,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-003.a2",
- "lineno": 53,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
+ "lineno": 15,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
- "lineno": 13,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
- "lineno": 14,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-17953562-004.a2",
- "lineno": 15,
- "level": "SERIOUS",
- "body": "unknown type: Exhibits"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
"lineno": 21,
@@ -4849,36 +4423,6 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
- "lineno": 37,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
- "lineno": 38,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
- "lineno": 39,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
- "lineno": 40,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-000.a2",
- "lineno": 41,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-001.a2",
"lineno": 31,
@@ -5156,50 +4700,32 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-010.a2",
- "lineno": 63,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-010.a2",
- "lineno": 64,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-010.a2",
- "lineno": 65,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-010.a2",
- "lineno": 66,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-011.a2",
+ "lineno": 30,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent OBT:004203 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-011.a2",
- "lineno": 39,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-011.a2",
- "lineno": 40,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-011.a2",
- "lineno": 41,
+ "lineno": 39,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-24010601-011.a2",
- "lineno": 42,
+ "lineno": 40,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
@@ -6175,6 +5701,18 @@
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
+ "lineno": 51,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
+ "lineno": 52,
+ "level": "SERIOUS",
+ "body": "unknown type: Lives_In"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
"lineno": 53,
@@ -6353,29 +5891,11 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
"lineno": 82,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
- "lineno": 83,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
- "lineno": 84,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
- "lineno": 85,
- "level": "SERIOUS",
"body": "unknown type: Exhibits"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25064656-013.a2",
- "lineno": 86,
+ "lineno": 83,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
@@ -6434,92 +5954,86 @@
"body": "unknown type: Lives_In"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 27,
- "level": "SERIOUS",
- "body": "unknown type: Lives_In"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 28,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-25955289-003.a2",
+ "lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: Lives_In"
+ "body": "referent OBT:004138 is not in the vocabulary"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 29,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 30,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 31,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 32,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 33,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 34,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 35,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 36,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 37,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 38,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 39,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 40,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: Lives_In"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-norm+ner\/a2\/BB-norm+ner-F-26187841-001.a2",
- "lineno": 41,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: Exhibits"
},
diff --git a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/eval.json
index bce7adb18d40fb6f6407001b098aa81e4322acaf..7f463475ff0b50796da0bcab0585627e05eda5b3 100644
--- a/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/eval.json
+++ b/corpora/BioNLP-OST-2019/batches/BB19-rel+ner/eval.json
@@ -1,6 +1,6 @@
{
"evaluation": {
- "submission-id": 706,
+ "submission-id": 709,
"global-evaluations": [{
"name": "Standard pairing",
"scorings": [
@@ -9,43 +9,43 @@
"measures": [
{
"name": "SER",
- "value": 1.3738019169329074
+ "value": 1.2917997870074547
},
{
"name": "ISER",
- "value": 0.4212651413189771
+ "value": 0.43633828996282525
},
{
"name": "Mismatches",
- "value": 55.8486470320888
+ "value": 53.01134053725426
},
{
"name": "Matches",
- "value": 219.15135296791124
+ "value": 215.9886594627458
},
{
"name": "Insertions",
- "value": 571
+ "value": 490
},
{
"name": "Deletions",
- "value": 664
+ "value": 670
},
{
"name": "F1",
- "value": 0.2455477344178277
+ "value": 0.2544036036074745
},
{
"name": "Recall",
- "value": 0.2333880223300439
+ "value": 0.23001987163231716
},
{
"name": "Precision",
- "value": 0.25904415244433954
+ "value": 0.2845700388178469
},
{
"name": "Predictions",
- "value": 846
+ "value": 759
}
]
},
@@ -54,43 +54,43 @@
"measures": [
{
"name": "SER",
- "value": 1.5341426403641882
+ "value": 1.417298937784522
},
{
"name": "ISER",
- "value": 0.3946107784431137
+ "value": 0.41368487131199
},
{
"name": "Mismatches",
- "value": 53.987434170875936
+ "value": 51.1501276760414
},
{
"name": "Matches",
- "value": 201.0125658291241
+ "value": 197.84987232395864
},
{
"name": "Insertions",
- "value": 554
+ "value": 473
},
{
"name": "Deletions",
- "value": 404
+ "value": 410
},
{
"name": "F1",
- "value": 0.2738590815110683
+ "value": 0.28653131401007764
},
{
"name": "Recall",
- "value": 0.30502665527939926
+ "value": 0.30022742386033174
},
{
"name": "Precision",
- "value": 0.24847041511634624
+ "value": 0.274030294077505
},
{
"name": "Predictions",
- "value": 809
+ "value": 722
}
]
},
@@ -99,43 +99,43 @@
"measures": [
{
"name": "SER",
- "value": 1.5534591194968554
+ "value": 1.4323899371069182
},
{
"name": "ISER",
- "value": 0.3916256157635468
+ "value": 0.4111182934712347
},
{
"name": "Mismatches",
- "value": 53.987434170875936
+ "value": 51.1501276760414
},
{
"name": "Matches",
- "value": 201.0125658291241
+ "value": 197.84987232395864
},
{
"name": "Insertions",
- "value": 554
+ "value": 473
},
{
"name": "Deletions",
- "value": 381
+ "value": 387
},
{
"name": "F1",
- "value": 0.27821808419255933
+ "value": 0.2913842007716622
},
{
"name": "Recall",
- "value": 0.316057493442019
+ "value": 0.31108470491188467
},
{
"name": "Precision",
- "value": 0.24847041511634624
+ "value": 0.274030294077505
},
{
"name": "Predictions",
- "value": 809
+ "value": 722
}
]
},
@@ -234,43 +234,43 @@
"measures": [
{
"name": "SER",
- "value": 1.3358585858585859
+ "value": 1.2512626262626263
},
{
"name": "ISER",
- "value": 0.4281081081081082
+ "value": 0.44419517666853614
},
{
"name": "Mismatches",
- "value": 53.84763488633981
+ "value": 51.010328391505276
},
{
"name": "Matches",
- "value": 208.15236511366027
+ "value": 204.9896716084948
},
{
"name": "Insertions",
- "value": 475
+ "value": 404
},
{
"name": "Deletions",
- "value": 530
+ "value": 536
},
{
"name": "F1",
- "value": 0.2722725508353961
+ "value": 0.28235491957092945
},
{
"name": "Recall",
- "value": 0.2628186428202781
+ "value": 0.2588253429400187
},
{
"name": "Precision",
- "value": 0.2824319743740302
+ "value": 0.3105904115280224
},
{
"name": "Predictions",
- "value": 737
+ "value": 660
}
]
},
@@ -279,43 +279,43 @@
"measures": [
{
"name": "SER",
- "value": 1.4908088235294117
+ "value": 1.3676470588235294
},
{
"name": "ISER",
- "value": 0.4014760147601476
+ "value": 0.422360248447205
},
{
"name": "Mismatches",
- "value": 51.98642202512695
+ "value": 49.14911553029241
},
{
"name": "Matches",
- "value": 190.0135779748731
+ "value": 186.8508844697076
},
{
"name": "Insertions",
- "value": 458
+ "value": 387
},
{
"name": "Deletions",
- "value": 302
+ "value": 308
},
{
"name": "F1",
- "value": 0.30548806748371876
+ "value": 0.3202243092882735
},
{
"name": "Recall",
- "value": 0.3492896653949873
+ "value": 0.34347589056931543
},
{
"name": "Precision",
- "value": 0.271447968535533
+ "value": 0.2999211628727249
},
{
"name": "Predictions",
- "value": 700
+ "value": 623
}
]
},
@@ -369,11 +369,11 @@
"measures": [
{
"name": "SER",
- "value": 1.3152289669861554
+ "value": 1.235356762513312
},
{
"name": "ISER",
- "value": 0.4319227230910764
+ "value": 0.4473558837541687
},
{
"name": "Mismatches",
@@ -381,31 +381,31 @@
},
{
"name": "Matches",
- "value": 275
+ "value": 269
},
{
"name": "Insertions",
- "value": 571
+ "value": 490
},
{
"name": "Deletions",
- "value": 664
+ "value": 670
},
{
"name": "F1",
- "value": 0.3081232492997199
+ "value": 0.3168433451118963
},
{
"name": "Recall",
- "value": 0.2928647497337593
+ "value": 0.28647497337593186
},
{
"name": "Precision",
- "value": 0.32505910165484636
+ "value": 0.3544137022397892
},
{
"name": "Predictions",
- "value": 846
+ "value": 759
}
]
},
@@ -414,11 +414,11 @@
"measures": [
{
"name": "SER",
- "value": 1.4537177541729893
+ "value": 1.339908952959029
},
{
"name": "ISER",
- "value": 0.40754483611626474
+ "value": 0.427367055771725
},
{
"name": "Mismatches",
@@ -426,31 +426,31 @@
},
{
"name": "Matches",
- "value": 255
+ "value": 249
},
{
"name": "Insertions",
- "value": 554
+ "value": 473
},
{
"name": "Deletions",
- "value": 404
+ "value": 410
},
{
"name": "F1",
- "value": 0.34741144414168934
+ "value": 0.3606082548877625
},
{
"name": "Recall",
- "value": 0.38694992412746587
+ "value": 0.37784522003034904
},
{
"name": "Precision",
- "value": 0.315203955500618
+ "value": 0.3448753462603878
},
{
"name": "Predictions",
- "value": 809
+ "value": 722
}
]
},
@@ -459,11 +459,11 @@
"measures": [
{
"name": "SER",
- "value": 1.470125786163522
+ "value": 1.3522012578616351
},
{
"name": "ISER",
- "value": 0.4048376830044557
+ "value": 0.4251336898395722
},
{
"name": "Mismatches",
@@ -471,31 +471,31 @@
},
{
"name": "Matches",
- "value": 255
+ "value": 249
},
{
"name": "Insertions",
- "value": 554
+ "value": 473
},
{
"name": "Deletions",
- "value": 381
+ "value": 387
},
{
"name": "F1",
- "value": 0.35294117647058826
+ "value": 0.36671575846833576
},
{
"name": "Recall",
- "value": 0.4009433962264151
+ "value": 0.3915094339622642
},
{
"name": "Precision",
- "value": 0.315203955500618
+ "value": 0.3448753462603878
},
{
"name": "Predictions",
- "value": 809
+ "value": 722
}
]
},
@@ -595,85 +595,49 @@
"messages": [
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10618167.a2",
- "lineno": 6,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10618167.a2",
- "lineno": 7,
+ "lineno": 5,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10618167.a2",
- "lineno": 8,
+ "lineno": 6,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10618167.a2",
- "lineno": 9,
+ "lineno": 7,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10618167.a2",
- "lineno": 10,
+ "lineno": 8,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 10,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 11,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 12,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 13,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 14,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 15,
+ "lineno": 5,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 16,
+ "lineno": 6,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 17,
+ "lineno": 7,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10645449.a2",
- "lineno": 18,
+ "lineno": 8,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -703,99 +667,93 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 17,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 18,
+ "lineno": 13,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 19,
+ "lineno": 14,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 20,
+ "lineno": 15,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 21,
+ "lineno": 16,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 22,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 23,
+ "lineno": 18,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 24,
+ "lineno": 19,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 25,
+ "lineno": 20,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 26,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 27,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 28,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 29,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 30,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
+ "lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 31,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
+ "lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10665543.a2",
- "lineno": 32,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
+ "lineno": 23,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
@@ -843,37 +801,37 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 33,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 35,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
"lineno": 36,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
@@ -899,42 +857,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 41,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 42,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 43,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 44,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 45,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10770276.a2",
- "lineno": 46,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-10792385.a2",
"lineno": 11,
@@ -1087,105 +1009,93 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 18,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 19,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 20,
+ "lineno": 15,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 21,
+ "lineno": 16,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 22,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 23,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 24,
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 25,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 26,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 27,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 28,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 29,
+ "lineno": 24,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 30,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 31,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 32,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 33,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-11551069.a2",
- "lineno": 34,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
+ "lineno": 25,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
@@ -1299,13 +1209,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
"lineno": 44,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
"lineno": 45,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
@@ -1326,16 +1236,34 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
- "lineno": 49,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
+ "lineno": 33,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12417169.a2",
- "lineno": 50,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
+ "lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
+ "lineno": 35,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
+ "lineno": 36,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
+ "lineno": 37,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
@@ -1455,109 +1383,49 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 57,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 58,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 59,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 60,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 61,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 62,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 63,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
"lineno": 64,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 65,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 66,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 67,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 68,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 69,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 70,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 71,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 72,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 73,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12438382.a2",
- "lineno": 74,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-12934822.a2",
@@ -1645,31 +1513,25 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14638480.a2",
- "lineno": 6,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14638480.a2",
- "lineno": 7,
+ "lineno": 5,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14638480.a2",
- "lineno": 8,
+ "lineno": 6,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14638480.a2",
- "lineno": 9,
+ "lineno": 7,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14638480.a2",
- "lineno": 10,
+ "lineno": 8,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -1701,7 +1563,7 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14657131.a2",
"lineno": 19,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-14657131.a2",
@@ -1757,12 +1619,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
- "lineno": 9,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
"lineno": 10,
@@ -1773,13 +1629,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
"lineno": 11,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
"lineno": 12,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
@@ -1805,6 +1661,24 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
+ "lineno": 17,
+ "level": "SERIOUS",
+ "body": "unknown type: NCBI_Taxonomy"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15273106.a2",
+ "lineno": 18,
+ "level": "SERIOUS",
+ "body": "unknown type: NCBI_Taxonomy"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
+ "lineno": 24,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
"lineno": 25,
@@ -1881,13 +1755,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
"lineno": 37,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
"lineno": 38,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
@@ -1937,18 +1811,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
- "lineno": 47,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15460321.a2",
- "lineno": 48,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-15612668.a2",
"lineno": 17,
@@ -2111,6 +1973,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
+ "lineno": 17,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
"lineno": 18,
@@ -2187,29 +2055,17 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
"lineno": 30,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
- "lineno": 31,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
- "lineno": 32,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
- "lineno": 33,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-1649682.a2",
- "lineno": 34,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -2485,57 +2341,45 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 10,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 11,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 12,
+ "lineno": 6,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 13,
+ "lineno": 7,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 14,
+ "lineno": 8,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 15,
+ "lineno": 9,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 16,
+ "lineno": 10,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 17,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
+ "lineno": 23,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-17261513.a2",
- "lineno": 18,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
+ "lineno": 24,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
@@ -2595,25 +2439,25 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
"lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
"lineno": 35,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
"lineno": 36,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
"lineno": 37,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
@@ -2658,28 +2502,28 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
- "lineno": 45,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
+ "lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
- "lineno": 46,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
+ "lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
- "lineno": 47,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
+ "lineno": 23,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19494280.a2",
- "lineno": 48,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
+ "lineno": 24,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
@@ -2691,49 +2535,49 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 26,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 27,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 28,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 29,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 30,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
"lineno": 33,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
@@ -2778,80 +2622,32 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 41,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
+ "lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 42,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
+ "lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 43,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
+ "lineno": 17,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 44,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
+ "lineno": 18,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 45,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 46,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 47,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-19656787.a2",
- "lineno": 48,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
- "lineno": 15,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
- "lineno": 16,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
- "lineno": 17,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
- "lineno": 18,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
- "lineno": 19,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20400104.a2",
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
@@ -2909,6 +2705,18 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
+ "lineno": 20,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
+ "lineno": 21,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
"lineno": 22,
@@ -2979,19 +2787,19 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
"lineno": 33,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
"lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
"lineno": 35,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
@@ -3011,30 +2819,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
- "lineno": 39,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
- "lineno": 40,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
- "lineno": 41,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-20672296.a2",
- "lineno": 42,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21148810.a2",
"lineno": 19,
@@ -3143,6 +2927,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
+ "lineno": 13,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
"lineno": 14,
@@ -3189,13 +2979,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
"lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
"lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
@@ -3210,16 +3000,16 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
- "lineno": 25,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
+ "lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21476570.a2",
- "lineno": 26,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
+ "lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
@@ -3363,55 +3153,43 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
"lineno": 56,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
"lineno": 57,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
"lineno": 58,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 59,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 60,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 61,
+ "lineno": 59,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 62,
+ "lineno": 60,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 63,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
+ "lineno": 10,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21511409.a2",
- "lineno": 64,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
+ "lineno": 11,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
@@ -3423,25 +3201,25 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
"lineno": 13,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
"lineno": 14,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
"lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
"lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
@@ -3456,28 +3234,16 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
- "lineno": 19,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
- "lineno": 20,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
- "lineno": 21,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
+ "lineno": 37,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-21989983.a2",
- "lineno": 22,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
+ "lineno": 38,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
@@ -3663,49 +3429,31 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
"lineno": 69,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
"lineno": 70,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 71,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 72,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 73,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 74,
+ "lineno": 71,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 75,
+ "lineno": 72,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22203552.a2",
- "lineno": 76,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
+ "lineno": 9,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
@@ -3741,25 +3489,19 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
"lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
"lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
- "lineno": 17,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-22537874.a2",
- "lineno": 18,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
+ "lineno": 24,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
@@ -3801,13 +3543,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
"lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
@@ -3894,16 +3636,22 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
- "lineno": 47,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
+ "lineno": 25,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-23645023.a2",
- "lineno": 48,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
+ "lineno": 26,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
+ "lineno": 27,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
@@ -3957,37 +3705,37 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 36,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 37,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 38,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 39,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 40,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
"lineno": 41,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
@@ -4031,42 +3779,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 49,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 50,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 51,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 52,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 53,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24389148.a2",
- "lineno": 54,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24584903.a2",
"lineno": 4,
@@ -4129,115 +3841,97 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 20,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 21,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 22,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 23,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 24,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 25,
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 26,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 27,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 28,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 29,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 30,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 31,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 32,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 33,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 34,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 35,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 36,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 37,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-24794581.a2",
- "lineno": 38,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -4297,213 +3991,165 @@
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 36,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 37,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 38,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 39,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 40,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 41,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 42,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 43,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 44,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 45,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 46,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 47,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 48,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 49,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 50,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 51,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 52,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 53,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 54,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 55,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 56,
+ "lineno": 39,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 57,
+ "lineno": 40,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 58,
+ "lineno": 41,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 59,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 60,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 61,
+ "lineno": 44,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 62,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 63,
+ "lineno": 46,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 64,
+ "lineno": 47,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 65,
+ "lineno": 48,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 66,
+ "lineno": 49,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 67,
+ "lineno": 50,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 68,
+ "lineno": 51,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 69,
+ "lineno": 52,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25046729.a2",
- "lineno": 70,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
+ "lineno": 34,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
@@ -4635,13 +4281,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
"lineno": 56,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
"lineno": 57,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
@@ -4697,18 +4343,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
- "lineno": 67,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25179651.a2",
- "lineno": 68,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25607366.a2",
"lineno": 3,
@@ -4721,6 +4355,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
+ "lineno": 25,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
"lineno": 26,
@@ -4755,13 +4395,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
"lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
@@ -4859,471 +4499,381 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
- "lineno": 49,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-25644009.a2",
- "lineno": 50,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 11,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 12,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 13,
+ "lineno": 9,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 14,
+ "lineno": 10,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 15,
+ "lineno": 11,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 16,
+ "lineno": 12,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 17,
+ "lineno": 13,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 18,
+ "lineno": 14,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 19,
+ "lineno": 15,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-26155675.a2",
- "lineno": 20,
+ "lineno": 16,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 27,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 28,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 29,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 30,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 31,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 32,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 33,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 34,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 35,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 36,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 37,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 38,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 39,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 40,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 41,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 42,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 43,
+ "lineno": 35,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 44,
+ "lineno": 36,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 45,
+ "lineno": 37,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 46,
+ "lineno": 38,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 47,
+ "lineno": 39,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 48,
+ "lineno": 40,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 49,
+ "lineno": 41,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 50,
+ "lineno": 42,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 51,
+ "lineno": 43,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-2617654.a2",
- "lineno": 52,
+ "lineno": 44,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 22,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 23,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 24,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 25,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 26,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 27,
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 28,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 29,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 30,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 31,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 32,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 33,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 34,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 35,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 36,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 37,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 38,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 39,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 40,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 41,
+ "lineno": 33,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3015879.a2",
- "lineno": 42,
+ "lineno": 34,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 20,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 21,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 22,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 23,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 24,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 25,
+ "lineno": 19,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 26,
+ "lineno": 20,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 27,
+ "lineno": 21,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 28,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 29,
+ "lineno": 23,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 30,
+ "lineno": 24,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 31,
+ "lineno": 25,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 32,
+ "lineno": 26,
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 33,
+ "lineno": 27,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 34,
+ "lineno": 28,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 35,
+ "lineno": 29,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 36,
+ "lineno": 30,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 37,
+ "lineno": 31,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-3516874.a2",
- "lineno": 38,
+ "lineno": 32,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -5453,6 +5003,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-817056.a2",
+ "lineno": 12,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-817056.a2",
"lineno": 13,
@@ -5511,18 +5067,6 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-817056.a2",
"lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-817056.a2",
- "lineno": 23,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-817056.a2",
- "lineno": 24,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
@@ -5609,6 +5153,18 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
+ "lineno": 29,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
+ "lineno": 30,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
"lineno": 31,
@@ -5715,25 +5271,25 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
"lineno": 48,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
"lineno": 49,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
"lineno": 50,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
"lineno": 51,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
@@ -5766,28 +5322,16 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
- "lineno": 57,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
- "lineno": 58,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
- "lineno": 59,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
+ "lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-8698477.a2",
- "lineno": 60,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
+ "lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
@@ -5823,25 +5367,25 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
"lineno": 28,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
"lineno": 29,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
"lineno": 30,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
@@ -5898,28 +5442,16 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
- "lineno": 41,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
- "lineno": 42,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 43,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9231420.a2",
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 44,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
@@ -6057,25 +5589,25 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 67,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 68,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 69,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
"lineno": 70,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
@@ -6162,28 +5694,22 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
- "lineno": 85,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
- "lineno": 86,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
+ "lineno": 40,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
- "lineno": 87,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
+ "lineno": 41,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9562874.a2",
- "lineno": 88,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
+ "lineno": 42,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
@@ -6237,37 +5763,37 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 51,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 52,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 53,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 54,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 55,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
"lineno": 56,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
@@ -6402,40 +5928,10 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 79,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 80,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 81,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 82,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 83,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9575437.a2",
- "lineno": 84,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
+ "lineno": 24,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
@@ -6555,29 +6051,17 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
"lineno": 44,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
- "lineno": 45,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
- "lineno": 46,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
- "lineno": 47,
+ "lineno": 45,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-9666962.a2",
- "lineno": 48,
+ "lineno": 46,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -6677,12 +6161,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
- "lineno": 35,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
"lineno": 36,
@@ -6771,7 +6249,7 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
"lineno": 50,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
@@ -6881,6 +6359,18 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
+ "lineno": 69,
+ "level": "SERIOUS",
+ "body": "unknown type: NCBI_Taxonomy"
+ },
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-001.a2",
+ "lineno": 70,
+ "level": "SERIOUS",
+ "body": "unknown type: NCBI_Taxonomy"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-002.a2",
"lineno": 11,
@@ -6941,6 +6431,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
+ "lineno": 12,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
"lineno": 13,
@@ -6981,13 +6477,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
"lineno": 19,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
"lineno": 20,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
@@ -7001,18 +6497,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
- "lineno": 23,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-003.a2",
- "lineno": 24,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-17953562-004.a2",
"lineno": 7,
@@ -7049,6 +6533,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
+ "lineno": 10,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
"lineno": 11,
@@ -7083,29 +6573,17 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
"lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
- "lineno": 17,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
- "lineno": 18,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
- "lineno": 19,
+ "lineno": 17,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-000.a2",
- "lineno": 20,
+ "lineno": 18,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -7613,6 +7091,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
+ "lineno": 19,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
"lineno": 20,
@@ -7683,13 +7167,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
"lineno": 31,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
"lineno": 32,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
@@ -7715,18 +7199,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
- "lineno": 37,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-24010601-011.a2",
- "lineno": 38,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-000.a2",
"lineno": 29,
@@ -9095,6 +8567,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
+ "lineno": 26,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
"lineno": 27,
@@ -9201,13 +8679,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
"lineno": 44,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
"lineno": 45,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
@@ -9239,18 +8717,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
- "lineno": 51,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2",
- "lineno": 52,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2",
"lineno": 14,
@@ -9419,6 +8885,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
+ "lineno": 28,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
"lineno": 29,
@@ -9507,13 +8979,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
"lineno": 43,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
"lineno": 44,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
@@ -9576,16 +9048,10 @@
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
- "lineno": 55,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2",
- "lineno": 56,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
+ "lineno": 9,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
@@ -9621,23 +9087,11 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
"lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
- "lineno": 16,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
- "lineno": 17,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2",
- "lineno": 18,
+ "lineno": 16,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -9665,6 +9119,12 @@
"level": "SERIOUS",
"body": "unknown type: OntoBiotope"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
+ "lineno": 9,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
"lineno": 10,
@@ -9699,25 +9159,19 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
"lineno": 15,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
"lineno": 16,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
- "lineno": 17,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-002.a2",
- "lineno": 18,
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
+ "lineno": 12,
"level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
+ "body": "unknown type: OntoBiotope"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
@@ -9771,23 +9225,11 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
"lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
- "lineno": 22,
- "level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
- "lineno": 23,
- "level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25955289-003.a2",
- "lineno": 24,
+ "lineno": 22,
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
@@ -9803,6 +9245,12 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
+ {
+ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
+ "lineno": 13,
+ "level": "SERIOUS",
+ "body": "unknown type: OntoBiotope"
+ },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
"lineno": 14,
@@ -9849,13 +9297,13 @@
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
"lineno": 21,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
"lineno": 22,
"level": "SERIOUS",
- "body": "unknown type: OntoBiotope"
+ "body": "unknown type: NCBI_Taxonomy"
},
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
@@ -9869,18 +9317,6 @@
"level": "SERIOUS",
"body": "unknown type: NCBI_Taxonomy"
},
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
- "lineno": 25,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
- {
- "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-001.a2",
- "lineno": 26,
- "level": "SERIOUS",
- "body": "unknown type: NCBI_Taxonomy"
- },
{
"source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-26187841-002.a2",
"lineno": 7,
diff --git a/corpora/cirm/BIA_2022/Omnicrobe_03-2022.xlsx b/corpora/cirm/BIA_2022/Omnicrobe_03-2022.xlsx
deleted file mode 100644
index 6c1b7acee0ff468fdd53219f13b0834cd071e657..0000000000000000000000000000000000000000
Binary files a/corpora/cirm/BIA_2022/Omnicrobe_03-2022.xlsx and /dev/null differ
diff --git a/corpora/cirm/CFBP_2022/ExportBaseCIRM-CFBP_Omnicrobe_8mars2022.xlsx b/corpora/cirm/CFBP_2022/ExportBaseCIRM-CFBP_Omnicrobe_8mars2022.xlsx
deleted file mode 100644
index 64f7fc1819302ed49fd7f4d1bafa144f93944253..0000000000000000000000000000000000000000
Binary files a/corpora/cirm/CFBP_2022/ExportBaseCIRM-CFBP_Omnicrobe_8mars2022.xlsx and /dev/null differ
diff --git a/corpora/cirm/Levures_2021/Florilege_23082021.xlsx b/corpora/cirm/Levures_2021/Florilege_23082021.xlsx
deleted file mode 100755
index 8e1202a032369432d3d9006eade9c052581f4856..0000000000000000000000000000000000000000
Binary files a/corpora/cirm/Levures_2021/Florilege_23082021.xlsx and /dev/null differ
diff --git a/corpora/cirm/README b/corpora/cirm/README
deleted file mode 100644
index 01907c423ea505b58f6991965aec0c99d603e4f6..0000000000000000000000000000000000000000
--- a/corpora/cirm/README
+++ /dev/null
@@ -1,3 +0,0 @@
-- données CIRM-BIA : 20 juillet 2021
-- données CIRM-Levures : 23 août 2021
-- données CIRM-CFBP : 17 juin 2021
diff --git a/corpora/dsmz/README b/corpora/dsmz/README
deleted file mode 100644
index 4f0b9e0b8647d07924e561ed00c7f5c151c66eb3..0000000000000000000000000000000000000000
--- a/corpora/dsmz/README
+++ /dev/null
@@ -1 +0,0 @@
-données DSMZ : 26 janvier 2018
diff --git a/corpora/genbank/README b/corpora/genbank/README
deleted file mode 100644
index 0fd10b08ff9c0b03392a605de6f68fc123ddd316..0000000000000000000000000000000000000000
--- a/corpora/genbank/README
+++ /dev/null
@@ -1 +0,0 @@
-- données GenBank : 01 novembre 2021
diff --git a/corpora/genbank/req1_sup800_bacteria-descriptors.csv b/corpora/genbank/req1_sup800_bacteria-descriptors.csv
deleted file mode 100644
index 3c331f616f021562d2eb5a0616e705dd319e5c1c..0000000000000000000000000000000000000000
Binary files a/corpora/genbank/req1_sup800_bacteria-descriptors.csv and /dev/null differ
diff --git a/docs/1-preprocess-ontology.md b/docs/1-preprocess-ontology.md
index 34d08c58ad2e2a22dd1c38894f77674397657594..4fa3dbdfe8c358ee742075b8f7d0086a4e8120c9 100644
--- a/docs/1-preprocess-ontology.md
+++ b/docs/1-preprocess-ontology.md
@@ -42,16 +42,16 @@ The pipeline relies on the following alvisnlp plans :
The pipeline handles the following resources :
* inputs
- * `ancillaries/BioNLP-OST+EnovFood.obo`
- * `ancillaries/ncbi-taxonomy/names.dmp`
+ * `share/BioNLP-OST+EnovFood.obo`
+ * `share/ncbi-taxonomy/names.dmp`
* outputs
- * `ancillaries/BioNLP-OST+EnovFood-Habitat.json`
- * `ancillaries/BioNLP-OST+EnovFood-Phenotype.json`
- * `ancillaries/Use_V2.json`
- * `ancillaries/BioNLP-OST+EnovFood-Habitat.tomap`
- * `ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap`
- * `ancillaries/food-process-lexicon.txt`
- * `ancillaries/NCBI_taxa_ontobiotope.txt`
+ * `share/BioNLP-OST+EnovFood-Habitat.json`
+ * `share/BioNLP-OST+EnovFood-Phenotype.json`
+ * `share/Use_V2.json`
+ * `share/BioNLP-OST+EnovFood-Habitat.tomap`
+ * `share/BioNLP-OST+EnovFood-Phenotype.tomap`
+ * `share/food-process-lexicon.txt`
+ * `share/NCBI_taxa_ontobiotope.txt`
* programs
* `alvisnlp singularity container`
* `conda env`
diff --git a/docs/2-generate-concept-path.md b/docs/2-generate-concept-path.md
index 1481d3a9764fcec6c6d31e44df9c44554e6aa27a..b53627336ba139ce1b57d9400b87aff55c4afe32 100644
--- a/docs/2-generate-concept-path.md
+++ b/docs/2-generate-concept-path.md
@@ -40,13 +40,13 @@ The pipeline use the following alvisnlp plan :
The pipeline handles the following resources :
* inputs
- * `ancillaries/BioNLP-OST+EnovFood-Habitat.obo`
- * `ancillaries/BioNLP-OST+EnovFood-Phenotype.obo`
- * `ancillaries/Use_V2.obo`
+ * `share/BioNLP-OST+EnovFood-Habitat.obo`
+ * `share/BioNLP-OST+EnovFood-Phenotype.obo`
+ * `share/Use_V2.obo`
* outputs
- * `ancillaries/BioNLP-OST+EnovFood-Habitat.paths`
- * `ancillaries/BioNLP-OST+EnovFood-Phenotype.paths`
- * `ancillaries/Use_V2.paths`
+ * `share/BioNLP-OST+EnovFood-Habitat.paths`
+ * `share/BioNLP-OST+EnovFood-Phenotype.paths`
+ * `share/Use_V2.paths`
* programs
* `alvisnlp singularity container`
diff --git a/docs/3-process-cirm-data.md b/docs/3-process-cirm-data.md
index 38c0554686522b82e06be609d2f04d609c024942..2449d7c3a51ede06ec0afbc878b49c2c51530583 100644
--- a/docs/3-process-cirm-data.md
+++ b/docs/3-process-cirm-data.md
@@ -39,8 +39,8 @@ The pipeline handles the following resources :
* `corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx`
* `corpora/cirm/Levures_2021/Florilege_21012021.xlsx`
* `corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
+ * `share/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+ * `share/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
* outputs
* `corpora/florilege/cirm/cirm-bia-results.txt`
* `corpora/florilege/cirm/cirm-yeast-results.txt`
diff --git a/docs/4-process-genbank-data.md b/docs/4-process-genbank-data.md
index a003de30df17d7f97af894b011ff9ec2cb256076..d3e8c2435c1826246926d9da701f1912b182e59b 100644
--- a/docs/4-process-genbank-data.md
+++ b/docs/4-process-genbank-data.md
@@ -36,9 +36,9 @@ The pipeline handles the following resources :
* inputs
* `/db/genbank/current/flat`
- * `ancillaries/ncbi-taxonomy-prefix/taxa+id_microorganisms.txt`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
+ * `share/ncbi-taxonomy-prefix/taxa+id_microorganisms.txt`
+ * `share/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+ * `share/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
* outputs
* `corpora/florilege/genbank/genbank-results.txt`
* programs
diff --git a/docs/5-process-dsmz-data.md b/docs/5-process-dsmz-data.md
index 484799acbf704a93bf3f7c44919ebe35b52299fa..ee7d495bcb22350ed07f3e03f49ba02ffeb21f27 100644
--- a/docs/5-process-dsmz-data.md
+++ b/docs/5-process-dsmz-data.md
@@ -48,7 +48,7 @@ The pipeline handles the following resources:
* inputs
* `corpora/dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv`
* `corpora/dsmz/dsmz-data/category=origin-key=sample_type.tsv`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
+ * `share/OntoBiotope_BioNLP-OST-2019-Phenotype.obo` ?
* outputs
* `corpora/dsmz/test.txt`
* programs
diff --git a/docs/6-process-pubmed-data.md b/docs/6-process-pubmed-data.md
index 5e016a1889d1f31d0c4c552c4ce46f4e7870f12d..a80d825b3e676370b32aa4a913e84bc4874bf197 100644
--- a/docs/6-process-pubmed-data.md
+++ b/docs/6-process-pubmed-data.md
@@ -57,17 +57,17 @@ The pipeline relies on the following alvisnlp plan:
The pipeline handles the following resources :
* inputs
* `corpora/pubmed`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
- * `ancillaries/OntoBiotope_BioNLP-OST-2019-Phenotype.obo`
- * `ancillaries/Use_V2.obo`
+ * `share/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+ * `share/OntoBiotope_BioNLP-OST-2019-Phenotype.obo`
+ * `share/Use_V2.obo`
* `ncbi-taxonomy-prefix/taxa+id_full.txt`
* `ncbi-taxonomy-prefix/taxid_microorganisms.txt`
* `ncbi-taxonomy-prefix/names.dmp`
* outputs
* `corpora/pubmed/expander`
* `corpora/pubmed/index`
- * `ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt`
- * `ancillaries/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt`
+ * `share/Florilege/2019-12-12/PubMed-Habitat-2019-12-12.txt`
+ * `share/Florilege/2019-12-12/PubMed-Phenotype-2019-12-12.txt`
* programs
* `alvisnlp singularity container`
* `python env`
diff --git a/docs/7-process-bionlp-ost.md b/docs/7-process-bionlp-ost.md
index edee115173e327e2614aaa38ae64945188069921..ee135c849aa3d848a965eda8ed6fa6f375f3b386 100644
--- a/docs/7-process-bionlp-ost.md
+++ b/docs/7-process-bionlp-ost.md
@@ -57,9 +57,9 @@ The pipeline relies on the following alvisnlp 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`
+ * `share/OntoBiotope_BioNLP-OST-2019-Habitat.obo`
+ * `share/OntoBiotope_BioNLP-OST-2019-Phenotype.obo`
+ * `share/Use_V2.obo`
* outputs
* `corpora/BioNLP-OST-2019/batch/*/eval.json`
* programs
diff --git a/docs/gestion_du_projet.md b/docs/gestion_du_projet.md
index 9a31087ddd22df563403e46fed287b13631420fb..b56407eae5ab011fef7d1b2ce3d078c59170cea7 100644
--- a/docs/gestion_du_projet.md
+++ b/docs/gestion_du_projet.md
@@ -18,7 +18,7 @@ Le projet contient plusieurs fichiers et dossiers importants. L'organisation du
* Le dossier **`plan/`** contient les plans d'exécution de AlvisNLP qui matérialisent les analyses spécifiques au text mining
* Le dossier **`corpora/`** doit contenir les données issues des différentes sources. Il doit également contenir les résultats finaux pour chaque source.
* Le dossier **`softwares/`** contient les environnements (conda), les scripts et les images (singularity) utilisés par les pipelines
-* Le dossier **`ancillaries/`** contient les ressources additionnelles et certaines résultats intermédiaires des pipelines
+* Le dossier **`share/`** contient les ressources additionnelles et certaines résultats intermédiaires des pipelines
* Le dossier **`config/`** contient les fichiers de configuration des pipelines. Ces fichiers donnent les valeurs aux paramètres et des options pour l'utilisation du cluster Migale
La suite de ce document décrit les procédures pour faire évoluer le workflow.
diff --git a/docs/run.md b/docs/run.md
index aea87dab6f28c56cb8899f0ebe1b042b12c5d160..43c51eaf09d2a510a6c40a10006670403b5d074e 100644
--- a/docs/run.md
+++ b/docs/run.md
@@ -21,15 +21,15 @@ Pubmed corpus is to split into several batches to put in the `corpora/pubmed/bat
## NCBI Taxonomy
NCBI taxonomy is required. The NCBI resources are generated using [BacDive Utils](https://forgemia.inra.fr/florilege/bacdive-utils)
-* NCBI taxa and ids (extended) : `ancillaries/supertaxo/taxa+id_full.txt`
-* NCBI taxa ids and synonyms : `ancillaries/supertaxo/taxid_microorganisms.txt`
-* NCBI taxa : `ancillaries/supertaxo/names.dmp`
-* NCBI-Bacdive Match : `ancillaries/supertaxo/bacdive-to-taxid.txt`
+* NCBI taxa and ids (extended) : `share/supertaxo/taxa+id_full.txt`
+* NCBI taxa ids and synonyms : `share/supertaxo/taxid_microorganisms.txt`
+* NCBI taxa : `share/supertaxo/names.dmp`
+* NCBI-Bacdive Match : `share/supertaxo/bacdive-to-taxid.txt`
## Expander
-* The expander config file (`ancillaries/expander.xml`) is required to create the index expander for AlvisIR in **step 6.**
-Edit file `ancillaries/expander.xml` to add correct paths
+* The expander config file (`share/expander.xml`) is required to create the index expander for AlvisIR in **step 6.**
+Edit file `share/expander.xml` to add correct paths
## Run the pipelines
The commands to run the steps look like the following. They must be executed from the project home dir with the `snakemake-5.13.0-env` activated.
diff --git a/process-evaluate_BioNLP-OST.snakefile b/evaluate_with_BioNLP-OST.snakefile
similarity index 79%
rename from process-evaluate_BioNLP-OST.snakefile
rename to evaluate_with_BioNLP-OST.snakefile
index 2d0213304e04ab1933811e1eff7906ebea81c8f3..be6cc03d042306b768de9aa9b7034fd1f0e4d768 100644
--- a/process-evaluate_BioNLP-OST.snakefile
+++ b/evaluate_with_BioNLP-OST.snakefile
@@ -1,4 +1,3 @@
-
## local rule
# localrules: all, concat_results
@@ -15,7 +14,9 @@ all
rule all:
input:
log=expand(config["BIONLPOST_BATCHES_HOME"] + "/{B}/eval.json", B=BATCHES),
- scores=expand(config["BIONLPOST_BATCHES_HOME"] + "/{B}/eval.json", B=BATCHES)
+ scores=expand(config["BIONLPOST_BATCHES_HOME"] + "/{B}/{B}-eval.json", B=BATCHES),
+ dest="corpora/florilege/eval/new"
+
'''
@@ -43,16 +44,16 @@ rule run_bionlp_prediction:
batch="{B}",
corpus='BioNLP-OST-2019',
onto_habitat=config["ONTOBIOTOPE_HABITAT"],
- tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
+ tomap_habitat='share/BioNLP-OST+EnovFood-Habitat.tomap',
onto_pheno=config["ONTOBIOTOPE_PHENOTYPE"],
- tomap_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ tomap_pheno='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
ontobiotopeUse=config["ONTOBIOTOPE_USE"],
plan='plans/omnicrobe_main.plan',
dir='corpora/BioNLP-OST-2019/batches/{B}/',
- taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt'
+ taxid_microorganisms='share/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ taxa_id_full='share/extended-microorganisms-taxonomy/taxa+id_full.txt'
singularity:config["SINGULARITY_IMG"]
shell:"""
rm -f {output.yatea_candidates} {output.yatea_var_candidates} && alvisnlp -J-XX:+UseSerialGC -J-Xmx25g -cleanTmp -verbose \
@@ -83,9 +84,20 @@ rule evaluate:
input:
zip=config["BIONLPOST_BATCHES_HOME"] + "/{B}/predictions.zip"
output:
- scores=config["BIONLPOST_BATCHES_HOME"] + "/{B}/eval.json"
+ scores=config["BIONLPOST_BATCHES_HOME"] + "/{B}/{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" """
+
+
+rule deposit:
+ input:
+ score=expand(config["BIONLPOST_BATCHES_HOME"] + "/{B}/{B}-eval.json", B=BATCHES)
+ output:
+ dest=directory("corpora/florilege/eval/new")
+ params:
+ date_time = now.strftime("%m-%d-%Y-%H-%M-%S")
+ shell:"""mkdir -p {output.dest} && cp -r {input.score} {output.dest}"""
+
\ No newline at end of file
diff --git a/plans/anaphora.plan b/plans/anaphora.plan
index 7604cf0fe1063b76f1c17038797914b3b9c0b8ad..e012921faa1cdc1927d079b6b7acc4b0f1b3f6d7 100644
--- a/plans/anaphora.plan
+++ b/plans/anaphora.plan
@@ -33,7 +33,7 @@
<coreferences>
<mono-anaphora>
<anaphora class="TabularProjector">
- <dictFile>ancillaries/anaphoraLexicon.txt</dictFile>
+ <dictFile>share/anaphoraLexicon.txt</dictFile>
<targetLayer>mono-anaphora</targetLayer>
<subject feature="form" layer="words"/>
<caseInsensitive>true</caseInsensitive>
@@ -266,7 +266,7 @@
<multi-ante-anaphora>
<bi-anaphora class="TabularProjector">
- <dictFile>ancillaries/biAnaphoraLexicon.txt</dictFile>
+ <dictFile>share/biAnaphoraLexicon.txt</dictFile>
<targetLayer>bi-anaphora</targetLayer>
<subject feature="form" layer="words"/>
<caseInsensitive>true</caseInsensitive>
diff --git a/plans/biotope_ontology_analyzer.plan b/plans/biotope_ontology_analyzer.plan
index 38e12f822ce566171759782d0e9f205327098a2a..ec5daccd4ccd8cf445615fea306ec7cc14c93526 100644
--- a/plans/biotope_ontology_analyzer.plan
+++ b/plans/biotope_ontology_analyzer.plan
@@ -11,7 +11,7 @@
<read-obo class="OBOReader">
- <oboFiles>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
<pathFeature>path</pathFeature>
</read-obo>
@@ -174,12 +174,12 @@
</POS-tag-correction4>
<analyze class="TomapTrain">
- <outFile>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</outFile>
+ <outFile>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</outFile>
<workingDir>yatea-train</workingDir>
<!--yateaExecutable>/usr/local/public/perl-5-24.0/bin/yatea</yateaExecutable-->
- <configDir>ancillaries/YaTeA/config-habitats</configDir>
- <localeDir>ancillaries/YaTeA/locale</localeDir>
- <rcFile>ancillaries/YaTeA/yatea.rc</rcFile>
+ <configDir>share/YaTeA/config-habitats</configDir>
+ <localeDir>share/YaTeA/locale</localeDir>
+ <rcFile>share/YaTeA/yatea.rc</rcFile>
<!--perlLib>/projet/mig/work/textemig/biotopes/software/yatea-lib</perlLib-->
<conceptIdentifier>document.@id</conceptIdentifier>
</analyze>
diff --git a/plans/food_process_lex.plan b/plans/food_process_lex.plan
index f5648c1dfd8e16d18db60b0e4137995898fb1a0b..f84bf14ac0480313610b9f0a2b7ba7be8ae621d8 100644
--- a/plans/food_process_lex.plan
+++ b/plans/food_process_lex.plan
@@ -11,7 +11,7 @@
</param>
<read-obo class="OBOReader">
- <oboFiles>ancillaries/OntoBiotope-v53zb-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope-v53zb-Habitat.obo</oboFiles>
<pathFeature>path</pathFeature>
</read-obo>
diff --git a/plans/geo.plan b/plans/geo.plan
index 7f0d8f7375384de56cedff5c38da2ce4c53952a6..57ca6771715275382e9fdf139e7e4f1000349118 100644
--- a/plans/geo.plan
+++ b/plans/geo.plan
@@ -7,7 +7,7 @@
</param>
<stanford class="StanfordNER">
- <classifierFile>ancillaries/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz</classifierFile>
+ <classifierFile>share/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz</classifierFile>
<labelFeature>stanford-label</labelFeature>
<targetLayer>stanford</targetLayer>
<searchInContents/>
diff --git a/plans/map_habitats.plan b/plans/map_habitats.plan
index 41498ac927cfee20370c808bebf61c45f3a02f7f..4aa060eaa33e08926951eadae87231b0cf0157cf 100644
--- a/plans/map_habitats.plan
+++ b/plans/map_habitats.plan
@@ -56,7 +56,7 @@
<!-- Project stopwords -->
<stopwordsprojector class="TabularProjector">
- <dictFile>ancillaries/stopwords_EN.txt</dictFile>
+ <dictFile>share/stopwords_EN.txt</dictFile>
<targetLayer>stopwords</targetLayer>
<valueFeatures>stopwords</valueFeatures>
<constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
@@ -87,7 +87,7 @@
<habitats>
<exact-match class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<targetLayer>habitats</targetLayer>
<subject layer="words" feature="form"/>
<idFeature>concept-id</idFeature>
@@ -97,7 +97,7 @@
</exact-match>
<exact-match-2 class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<targetLayer>habitats2</targetLayer>
<subject layer="words" feature="lemma"/>
<idFeature>concept-id</idFeature>
@@ -114,7 +114,7 @@
</add-exact-2>
<exact-match-3 class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<targetLayer>habitats3</targetLayer>
<subject layer="words" feature="lemma2"/>
<idFeature>concept-id</idFeature>
@@ -131,7 +131,7 @@
</add-exact-3>
<exact-match-4 class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<targetLayer>habitats4</targetLayer>
<subject layer="words" feature="variant"/>
<idFeature>concept-id</idFeature>
diff --git a/plans/omnicrobe_main.plan b/plans/omnicrobe_main.plan
index 453072cf0a224c1354419a5b0e37fa3e74530dc9..73d9ac5bd0c25a62dc3a804bdd54685179380364 100644
--- a/plans/omnicrobe_main.plan
+++ b/plans/omnicrobe_main.plan
@@ -169,7 +169,7 @@
<read>
<pubmed class="XMLReader">
<source>corpora/pubmed/batches/0001/batch.xml</source>
- <xslTransform>ancillaries/microbes-2019-pubmed2alvisnlp.xslt</xslTransform>
+ <xslTransform>share/microbes-2019-pubmed2alvisnlp.xslt</xslTransform>
<constantDocumentFeatures>batch=0001</constantDocumentFeatures>
</pubmed>
@@ -186,7 +186,7 @@
</assert>
<mesh-path class="FileMapper">
- <mappingFile>ancillaries/2017MeshTree.txt</mappingFile>
+ <mappingFile>share/2017MeshTree.txt</mappingFile>
<target>documents.(sections:mesh|sections:chemical)</target>
<form>@UI</form>
<targetFeatures>mesh-path,,mesh-name</targetFeatures>
diff --git a/plans/phenotype_ontology_analyzer.plan b/plans/phenotype_ontology_analyzer.plan
index 1eeb430f86fd83b0f0431ecad4a29c1c4a2459e4..f62e6b61bf9226df137ee247d3370ae569b445e3 100644
--- a/plans/phenotype_ontology_analyzer.plan
+++ b/plans/phenotype_ontology_analyzer.plan
@@ -139,9 +139,9 @@
<outFile>resources/OntoBiotope_BioNLP-OST-2019-Phenotype.tomap</outFile>
<workingDir>yatea-train</workingDir>
<!--yateaExecutable>/usr/local/public/perl-5-24.0/bin/yatea</yateaExecutable-->
- <configDir>ancillaries/YaTeA/config-habitats</configDir>
- <localeDir>ancillaries/YaTeA/locale</localeDir>
- <rcFile>ancillaries/YaTeA/yatea.rc</rcFile>
+ <configDir>share/YaTeA/config-habitats</configDir>
+ <localeDir>share/YaTeA/locale</localeDir>
+ <rcFile>share/YaTeA/yatea.rc</rcFile>
<!--perlLib>/projet/mig/work/textemig/biotopes/software/yatea-lib</perlLib-->
<conceptIdentifier>document.@id</conceptIdentifier>
</analyze>
diff --git a/plans/stopwords.plan b/plans/stopwords.plan
index 087e68bed9dc92802542f2a7f7bef51a80495f31..0330e5d8c58f0b45d37586587cd1f8fd2ef99b2f 100644
--- a/plans/stopwords.plan
+++ b/plans/stopwords.plan
@@ -3,7 +3,7 @@
<alvisnlp-plan id="stopwords">
<stopwordsprojector class="TabularProjector">
- <dictFile>ancillaries/stopwords_EN.txt</dictFile>
+ <dictFile>share/stopwords_EN.txt</dictFile>
<targetLayer>stopwords</targetLayer>
<valueFeatures>stopwords</valueFeatures>
<constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
@@ -11,7 +11,7 @@
</stopwordsprojector>
<stopwordsprojector-microorganism class="TabularProjector">
- <dictFile>ancillaries/microorganism_stopwords.txt</dictFile>
+ <dictFile>share/microorganism_stopwords.txt</dictFile>
<targetLayer>microorganism-stopwords</targetLayer>
<valueFeatures>stopwords</valueFeatures>
<constantAnnotationFeatures>ne-type=stopwords</constantAnnotationFeatures>
diff --git a/plans/strains-2.plan b/plans/strains-2.plan
index f30ffb5baea5c705e46be7c3e2d28530a5279323..c41cf30e349d5a03c0d24e1aa5a31ff0fb43f792 100644
--- a/plans/strains-2.plan
+++ b/plans/strains-2.plan
@@ -317,7 +317,7 @@
<module id="species2" class="SimpleProjector2">
<caseInsensitive/>
<valueFeatures>microbe</valueFeatures>
- <dictFile>ancillaries/microbes_v4.txt</dictFile>
+ <dictFile>share/microbes_v4.txt</dictFile>
<targetLayer>species__additional</targetLayer>
<constantAnnotationFeatures>type=Bacteria,eos=not-eos,ne-type=species,pos=NP</constantAnnotationFeatures>
</module>
diff --git a/plans/tag_ncbi_common_names.plan b/plans/tag_ncbi_common_names.plan
index 57b61330789e3be7427857a47a22e3268f63a685..a4587c0b8b1ec8384c7c80b994c4e8eab50cdc82 100644
--- a/plans/tag_ncbi_common_names.plan
+++ b/plans/tag_ncbi_common_names.plan
@@ -23,7 +23,7 @@
</param>
<read class="TabularReader">
- <source>ancillaries/NCBI_common_names</source>
+ <source>share/NCBI_common_names</source>
<sourceElement>$</sourceElement>
<lineActions separator=";">
new:document(tab:column(0) ^ "-" ^ tab:column(1)).(
@@ -152,28 +152,28 @@
<!-- Run Yatea term extractor -->
<yatea class="YateaExtractor">
- <xmlTermsFile>ancillaries/yatea-ncbi/candidates.xml</xmlTermsFile>
+ <xmlTermsFile>share/yatea-ncbi/candidates.xml</xmlTermsFile>
<posFeature>pos</posFeature>
- <configDir>ancillaries/YaTeA/config-habitats</configDir>
- <localeDir>ancillaries/YaTeA/locale</localeDir>
- <rcFile>ancillaries/YaTeA/yatea.rc</rcFile>
+ <configDir>share/YaTeA/config-habitats</configDir>
+ <localeDir>share/YaTeA/locale</localeDir>
+ <rcFile>share/YaTeA/yatea.rc</rcFile>
<!--perlLib>/projet/mig/work/textemig/biotopes/software/yatea-lib</perlLib-->
</yatea>
<!-- ToMap on lemmas -->
<tomap class="TomapProjector">
- <yateaFile output-feed="true">ancillaries/yatea-ncbi/candidates.xml</yateaFile>
+ <yateaFile output-feed="true">share/yatea-ncbi/candidates.xml</yateaFile>
<targetLayerName>habitats</targetLayerName>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats</target>
<form>@concept-id</form>
@@ -185,18 +185,18 @@
<tomap-on-alternative-lemmas>
<tomap class="TomapProjector">
- <yateaFile output-feed="true">ancillaries/yatea-ncbi/candidates.xml</yateaFile>
+ <yateaFile output-feed="true">share/yatea-ncbi/candidates.xml</yateaFile>
<targetLayerName>habitats2</targetLayerName>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma2" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats2</target>
<form>@concept-id</form>
@@ -217,17 +217,17 @@
<tomap-no-lemmakeys>
<tomap class="TomapProjector">
- <yateaFile output-feed="true">ancillaries/yatea-ncbi/candidates.xml</yateaFile>
+ <yateaFile output-feed="true">share/yatea-ncbi/candidates.xml</yateaFile>
<targetLayerName>habitats3</targetLayerName>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats3</target>
<form>@concept-id</form>
@@ -248,17 +248,17 @@
<tomap-no-lemmakeys-word-form>
<tomap class="TomapProjector">
- <yateaFile output-feed="true">ancillaries/yatea-ncbi/candidates.xml</yateaFile>
+ <yateaFile output-feed="true">share/yatea-ncbi/candidates.xml</yateaFile>
<targetLayerName>habitats5</targetLayerName>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/OntoBiotope_BioNLP-OST-2019-Habitat.tomap</tomapClassifier>
<subject feature="form" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
+ <oboFiles>share/OntoBiotope_BioNLP-OST-2019-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats5</target>
<form>@concept-id</form>
@@ -285,7 +285,7 @@
<!-- Projet Yatea results -->
<yatea-proj id="yatea-projection" class="YateaTermsProjector">
<targetLayerName>yateaTerms</targetLayerName>
- <yateaFile output-feed="yes">ancillaries/yatea-ncbi/candidates.xml</yateaFile>
+ <yateaFile output-feed="yes">share/yatea-ncbi/candidates.xml</yateaFile>
<subject layer="words"/>
<termLemma>lemma</termLemma>
</yatea-proj>
@@ -351,7 +351,7 @@
<!-- Remove terms with blacklisted syntactic heads -->
<delete-blacklisted-heads class="Action">
- <target>documents.sections.layer:habitats[@explain_significant-head in "ancillaries/blacklisted-heads.txt" and not (@concept-name =~ " " and (str:lower(@lemma-string) ?= str:lower(@concept-name) or @score == "1.0"))]</target>
+ <target>documents.sections.layer:habitats[@explain_significant-head in "share/blacklisted-heads.txt" and not (@concept-name =~ " " and (str:lower(@lemma-string) ?= str:lower(@concept-name) or @score == "1.0"))]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-blacklisted-heads>
@@ -456,7 +456,7 @@
<!-- remove blacklisted terms -->
<delete-blacklisted class="Action">
- <target>documents.sections.layer:habitats[@selected == "true" and @lemma-string in "ancillaries/blacklist.txt"]</target>
+ <target>documents.sections.layer:habitats[@selected == "true" and @lemma-string in "share/blacklist.txt"]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-blacklisted>
diff --git a/plans/taxa.plan b/plans/taxa.plan
index 8df9b6f72a33b365681f65b67fd68d139dcd2aa5..a0f018ac172d2010dcc2b47db8592cde4235c4db 100644
--- a/plans/taxa.plan
+++ b/plans/taxa.plan
@@ -17,8 +17,8 @@
<dict class="TabularProjector">
<targetLayer>ambiguous-taxa</targetLayer>
- <!--<dictFile>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>-->
- <trieSource>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.trie</trieSource>
+ <!--<dictFile>share/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>-->
+ <trieSource>share/extended-microorganisms-taxonomy/taxa+id_full.trie</trieSource>
<substituteWhitespace/>
<valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
<constantAnnotationFeatures>source=NCBI,not-ambiguous=no</constantAnnotationFeatures>
@@ -79,7 +79,7 @@
<default-disambiguation>
<map class="FileMapper">
- <mappingFile>ancillaries/default-taxon-disambiguation.txt</mappingFile>
+ <mappingFile>share/default-taxon-disambiguation.txt</mappingFile>
<target>documents.sections.layer:taxa[@not-ambiguous != "yes" and not (span:taxa[@not-ambiguous == "yes"])]</target>
<form>@form</form>
<targetFeatures>,default-taxid</targetFeatures>
diff --git a/plans/term-extraction.plan b/plans/term-extraction.plan
index 00407ffa4e5adf276a2410f6c18fa1e7ef50391e..279ecd53c21085461586bebaea7a8fb12a48f4ee 100644
--- a/plans/term-extraction.plan
+++ b/plans/term-extraction.plan
@@ -19,7 +19,7 @@
<!-- Project variant lexicon on words and add variant feature -->
<variant-projection class="TabularProjector">
- <dictFile>ancillaries/noun_adj_and_spelling_variants</dictFile>
+ <dictFile>share/noun_adj_and_spelling_variants</dictFile>
<targetLayer>variants</targetLayer>
<keyIndex>0</keyIndex>
<valueFeatures>string,variant</valueFeatures>
@@ -49,9 +49,9 @@
<sectionFilter>@name == "title" or @name == "abstract"</sectionFilter>
<xmlTermsFile>yatea/candidates.xml</xmlTermsFile>
<posFeature>pos</posFeature>
- <configDir>ancillaries/YaTeA/config-habitats</configDir>
- <localeDir>ancillaries/YaTeA/locale</localeDir>
- <rcFile>ancillaries/YaTeA/yatea.rc</rcFile>
+ <configDir>share/YaTeA/config-habitats</configDir>
+ <localeDir>share/YaTeA/locale</localeDir>
+ <rcFile>share/YaTeA/yatea.rc</rcFile>
<!--perlLib>/projet/mig/work/textemig/biotopes/software/yatea-lib</perlLib-->
</yatea>
@@ -61,9 +61,9 @@
<xmlTermsFile>yatea-var/candidates.xml</xmlTermsFile>
<posFeature>pos</posFeature>
<lemmaFeature>variant</lemmaFeature>
- <configDir>ancillaries/YaTeA/config-habitats</configDir>
- <localeDir>ancillaries/YaTeA/locale</localeDir>
- <rcFile>ancillaries/YaTeA/yatea.rc</rcFile>
+ <configDir>share/YaTeA/config-habitats</configDir>
+ <localeDir>share/YaTeA/locale</localeDir>
+ <rcFile>share/YaTeA/yatea.rc</rcFile>
<!--perlLib>/projet/mig/work/textemig/biotopes/software/yatea-lib</perlLib-->
</yatea-var>
diff --git a/plans/tomap-habitats.plan b/plans/tomap-habitats.plan
index 701b32b7a2153774773c0663be4da11262f7104c..ce908ff77c159546c5c3b6c193ff6c4e90281ebe 100644
--- a/plans/tomap-habitats.plan
+++ b/plans/tomap-habitats.plan
@@ -5,7 +5,7 @@
<food-process-dict class="TabularProjector">
<targetLayer>food-process</targetLayer>
- <dictFile>ancillaries/food-process-lexicon.txt</dictFile>
+ <dictFile>share/food-process-lexicon.txt</dictFile>
<matchStartCaseInsensitive/>
<keyIndex>0,1,2</keyIndex>
<valueFeatures>string,token,lem,concept-id</valueFeatures>
@@ -22,14 +22,14 @@
<targetLayer>habitats</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats</target>
<form>@concept-id</form>
@@ -45,14 +45,14 @@
<targetLayer>habitats2</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma2" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats2</target>
<form>@concept-id</form>
@@ -77,13 +77,13 @@
<targetLayer>habitats3</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats3</target>
<form>@concept-id</form>
@@ -108,14 +108,14 @@
<targetLayer>habitats4</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="variant" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats4</target>
<form>@concept-id</form>
@@ -140,13 +140,13 @@
<targetLayer>habitats5</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" graylist="share/graylist_extended.heads" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
<subject feature="form" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats5</target>
<form>@concept-id</form>
@@ -268,7 +268,7 @@
<!-- Remove terms with blacklisted syntactic heads -->
<delete-blacklisted-heads class="Action">
- <target>documents.sections.layer:habitats[str:lower(@explain_significant-head) in "ancillaries/blacklisted-heads.txt" and not (@concept-name =~ " " and (str:lower(@lemma-string) ?= str:lower(@concept-name) or @score == "1.0"))]</target>
+ <target>documents.sections.layer:habitats[str:lower(@explain_significant-head) in "share/blacklisted-heads.txt" and not (@concept-name =~ " " and (str:lower(@lemma-string) ?= str:lower(@concept-name) or @score == "1.0"))]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-blacklisted-heads>
@@ -305,12 +305,12 @@
<removeFromLayer/>
</delete-plant-others>
<delete-fake-walls class="Action">
- <target>documents.sections.layer:habitats[str:lower(@lemma-string) in "ancillaries/not-walls.txt" and @concept-path =~ "OBT:000466"]</target>
+ <target>documents.sections.layer:habitats[str:lower(@lemma-string) in "share/not-walls.txt" and @concept-path =~ "OBT:000466"]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-fake-walls>
<delete-fake-trees class="Action">
- <target>documents.sections.layer:habitats[str:lower(@lemma-string) in "ancillaries/not-trees.txt" and @concept-path =~ "OBT:001360"]</target>
+ <target>documents.sections.layer:habitats[str:lower(@lemma-string) in "share/not-trees.txt" and @concept-path =~ "OBT:001360"]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-fake-trees>
@@ -522,7 +522,7 @@
<!-- remove blacklisted terms -->
<delete-blacklisted class="Action">
- <target>documents.sections.layer:habitats[@selected == "true" and str:lower(@lemma-string) in "ancillaries/blacklist.txt"]</target>
+ <target>documents.sections.layer:habitats[@selected == "true" and str:lower(@lemma-string) in "share/blacklist.txt"]</target>
<action>remove:habitats</action>
<removeFromLayer/>
</delete-blacklisted>
@@ -634,7 +634,7 @@
<!-- map some of the living organisms to more specific concepts -->
<map-living-organisms class="FileMapper">
- <mappingFile>ancillaries/NCBI_taxa_ontobiotope.txt</mappingFile>
+ <mappingFile>share/NCBI_taxa_ontobiotope.txt</mappingFile>
<target>documents.sections.layer:habitats[@taxid != ""]</target>
<form>@taxid</form>
<keyColumn>1</keyColumn>
@@ -722,7 +722,7 @@
<!-- Add concept-path in case some are missing -->
<concept-path class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:habitats</target>
<form>@concept-id</form>
diff --git a/plans/tomap-microbial-phenotypes.plan b/plans/tomap-microbial-phenotypes.plan
index bc9813610add4cfbcfa26f45538449e9d488abc3..f416715ea534ac3482c60a526b10783046343ffa 100644
--- a/plans/tomap-microbial-phenotypes.plan
+++ b/plans/tomap-microbial-phenotypes.plan
@@ -6,14 +6,14 @@
<targetLayer>phenotypes</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes</target>
<form>@concept-id</form>
@@ -29,14 +29,14 @@
<targetLayer>phenotypes2</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="lemma2" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes2</target>
<form>@concept-id</form>
@@ -61,13 +61,13 @@
<targetLayer>phenotypes3</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
<subject feature="lemma" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes3</target>
<form>@concept-id</form>
@@ -93,14 +93,14 @@
<targetLayer>phenotypes4</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
<lemmaKeys/>
<subject feature="variant" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes4</target>
<form>@concept-id</form>
@@ -125,13 +125,13 @@
<targetLayer>phenotypes5</targetLayer>
<conceptFeature>concept-id</conceptFeature>
<explanationFeaturePrefix>explain_</explanationFeaturePrefix>
- <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+ <tomapClassifier empty-words="share/stopwords_EN.ttg" whole-proxy-distance="false">share/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
<subject feature="form" layer="words"/>
<scoreFeature>score</scoreFeature>
</tomap>
<concept-names class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes5</target>
<form>@concept-id</form>
@@ -223,7 +223,7 @@
<!-- Remove terms with blacklisted syntactic heads -->
<delete-blacklisted-heads class="Action">
- <target>documents.sections.layer:phenotypes[@explain_significant-head in "ancillaries/blacklisted-phenotype-heads.txt" and not (@concept-name =~ " " and (@lemma-string ?= @concept-name or @score == "1.0"))]</target>
+ <target>documents.sections.layer:phenotypes[@explain_significant-head in "share/blacklisted-phenotype-heads.txt" and not (@concept-name =~ " " and (@lemma-string ?= @concept-name or @score == "1.0"))]</target>
<action>remove:phenotypes</action>
<removeFromLayer/>
</delete-blacklisted-heads>
@@ -323,7 +323,7 @@
<!-- remove blacklisted terms -->
<delete-blacklisted class="Action">
- <target>documents.sections.layer:phenotypes[@selected == "true" and @lemma-string in "ancillaries/phenotype_blacklist.txt"]</target>
+ <target>documents.sections.layer:phenotypes[@selected == "true" and @lemma-string in "share/phenotype_blacklist.txt"]</target>
<action>remove:phenotypes</action>
<removeFromLayer/>
</delete-blacklisted>
@@ -394,7 +394,7 @@
<!-- <idFeature>molecule-id</idFeature> -->
<!-- <nameFeature>molecule-name</nameFeature> -->
<!-- <pathFeature>molecule-path</pathFeature> -->
- <!-- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
+ <!-- <oboFiles>share/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
<!-- <subject feature="lemma" layer="words"/> -->
<!-- <targetLayer>molecules</targetLayer> -->
<!-- </molecule-projection-on-lemmas> -->
@@ -404,7 +404,7 @@
<!-- <idFeature>molecule-id</idFeature> -->
<!-- <nameFeature>molecule-name</nameFeature> -->
<!-- <pathFeature>molecule-path</pathFeature> -->
- <!-- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
+ <!-- <oboFiles>share/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
<!-- <subject feature="form" layer="words"/> -->
<!-- <targetLayer>molecules2</targetLayer> -->
<!-- </molecule-projection-on-words> -->
@@ -469,7 +469,7 @@
<!-- Add concept-path in case some are missing -->
<concept-path class="OBOMapper">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
<idKeys/>
<target>documents.sections.layer:phenotypes</target>
<form>@concept-id</form>
diff --git a/plans/use-extraction.plan b/plans/use-extraction.plan
index 814224de47fbceec24fa48c17a970da2bab4eb95..9b5e277952eeefcf49818a3aa2445ec9087eb4fc 100644
--- a/plans/use-extraction.plan
+++ b/plans/use-extraction.plan
@@ -2,7 +2,7 @@
<alvisnlp-plan id="Use-extraction">
<exact-match class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Use.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Use.obo</oboFiles>
<targetLayer>uses</targetLayer>
<subject feature="form" layer="words"/>
<idFeature>concept-id</idFeature>
@@ -12,7 +12,7 @@
</exact-match>
<exact-match-2 class="OBOProjector">
- <oboFiles>ancillaries/BioNLP-OST+EnovFood-Use.obo</oboFiles>
+ <oboFiles>share/BioNLP-OST+EnovFood-Use.obo</oboFiles>
<targetLayer>uses2</targetLayer>
<subject feature="lemma" layer="words"/>
<idFeature>concept-id</idFeature>
diff --git a/preprocess-ontology.snakefile b/preprocess-Ontobiotope.snakefile
similarity index 72%
rename from preprocess-ontology.snakefile
rename to preprocess-Ontobiotope.snakefile
index f5dc7d62c828aebbbbcc57212495d9678f30f382..94ead35b97d554e7e399e0417424fb7baef991ab 100644
--- a/preprocess-ontology.snakefile
+++ b/preprocess-Ontobiotope.snakefile
@@ -1,3 +1,8 @@
+import time
+
+# Save timestamp
+start = time.time()
+
## config file
configfile: "config/config.yaml"
@@ -21,14 +26,17 @@ rule all:
'corpora/florilege/alvisir/BioNLP-OST+EnovFood-Habitat.json',
'corpora/florilege/alvisir/BioNLP-OST+EnovFood-Phenotype.json',
'corpora/florilege/alvisir/BioNLP-OST+EnovFood-Use.json',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- 'ancillaries/food-process-lexicon.txt',
- 'ancillaries/NCBI_taxa_ontobiotope.txt',
- 'ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
- 'ancillaries/BioNLP-OST+EnovFood-Use.obo',
- expand("ancillaries/{ontoname}.paths", ontoname=ONTONAMES.split(' '))
+ 'share/BioNLP-OST+EnovFood-Habitat.tomap',
+ 'share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ 'share/food-process-lexicon.txt',
+ 'share/NCBI_taxa_ontobiotope.txt',
+ 'share/BioNLP-OST+EnovFood-Habitat.obo',
+ 'share/BioNLP-OST+EnovFood-Phenotype.obo',
+ 'share/BioNLP-OST+EnovFood-Use.obo',
+ expand("share/{ontoname}.paths", ontoname=ONTONAMES.split(' ')),
+ #yatea_candidates='share/yatea/candidates.xml',
+ #yatea_var_candidates='share/yatea-var/candidates.xml',
+ yatea_ncbi= 'share/yatea-ncbi/candidates.xml'
'''
@@ -38,7 +46,7 @@ rule remove_obsolete_concepts:
input:
onto=config['ONTOBIOTOPE']
output:
- onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
+ onto='share/BioNLP-OST+EnovFood-no-obsolete.obo'
conda: 'softwares/envs/obo-utils-env.yaml'
shell: 'python softwares/obo-utils/obo2obo.py {input.onto} > {output.onto}'
@@ -48,9 +56,9 @@ Cut Habitat subtree
'''
rule cut_subtrees_habitat:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
+ onto='share/BioNLP-OST+EnovFood-no-obsolete.obo'
output:
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo'
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo'
params:
habitat_root=config['HABITAT_ROOT']
conda: 'softwares/envs/obo-utils-env.yaml'
@@ -66,9 +74,9 @@ Cut Phenotype subtree
'''
rule cut_subtrees_phenotype:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
+ onto='share/BioNLP-OST+EnovFood-no-obsolete.obo'
output:
- onto='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo'
+ onto='share/BioNLP-OST+EnovFood-Phenotype.obo'
params:
phenotype_root=config['PHENOTYPE_ROOT']
conda: 'softwares/envs/obo-utils-env.yaml'
@@ -84,9 +92,9 @@ Cut Use subtree
'''
rule cut_subtrees_use:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-no-obsolete.obo'
+ onto='share/BioNLP-OST+EnovFood-no-obsolete.obo'
output:
- onto='ancillaries/BioNLP-OST+EnovFood-Use.obo'
+ onto='share/BioNLP-OST+EnovFood-Use.obo'
conda: 'softwares/envs/obo-utils-env.yaml'
params:
use_root=config['USE_ROOT']
@@ -103,9 +111,9 @@ Analyze ontologies with tomap
'''
rule analyze_onto_Habitat:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo'
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo'
output:
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap'
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap'
params:
plan='plans/biotope_ontology_analyzer.plan',
tmpDir=config['TMP']
@@ -122,9 +130,9 @@ Analyze ontologies with tomap
'''
rule analyze_onto_phenotype:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo'
+ onto='share/BioNLP-OST+EnovFood-Phenotype.obo'
output:
- tomap='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap'
+ tomap='share/BioNLP-OST+EnovFood-Phenotype.tomap'
params:
plan='plans/phenotype_ontology_analyzer.plan',
tmpDir=config['TMP']
@@ -142,9 +150,9 @@ Build food process lexicon
'''
rule build_food_process_lexicon:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo'
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo'
output:
- lexicon='ancillaries/food-process-lexicon.txt'
+ lexicon='share/food-process-lexicon.txt'
params:
plan='plans/food_process_lex.plan',
tmpDir=config['TMP']
@@ -163,7 +171,7 @@ rule get_ncbi_names:
input:
names=config['NCBI_TAXO_NAMES']
output:
- common_names='ancillaries/NCBI_common_names'
+ common_names='share/NCBI_common_names'
shell: 'grep "common name" {input.names} |cut -f1,2 -d"|" |perl -npe "s/\s+\|\s+/\t/; s/\s+\n/\n/;" > {output.common_names}'
'''
@@ -171,15 +179,16 @@ build name lexicon
'''
rule build_ncbi_common_name_lexicon:
input:
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- common_names='ancillaries/NCBI_common_names',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg'
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ common_names='share/NCBI_common_names',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg'
output:
- taxa='ancillaries/NCBI_taxa_ontobiotope.txt',
- yatea_candidates='/ancillaries/yatea/candidates.xml',
- yatea_var_candidates='/ancillaries/yatea-var/candidates.xml'
+ taxa='share/NCBI_taxa_ontobiotope.txt',
+ #yatea_candidates='share/yatea/candidates.xml',
+ #yatea_var_candidates='share/yatea-var/candidates.xml',
+ yatea_ncbi= 'share/yatea-ncbi/candidates.xml'
params:
plan='plans/tag_ncbi_common_names.plan',
tmpDir=config['TMP']
@@ -197,7 +206,7 @@ obo to json
'''
rule convert_obo2json_habitat:
input:
- obo='ancillaries/BioNLP-OST+EnovFood-Habitat.obo'
+ obo='share/BioNLP-OST+EnovFood-Habitat.obo'
output:
json='corpora/florilege/alvisir/BioNLP-OST+EnovFood-Habitat.json'
params:
@@ -210,7 +219,7 @@ convert phenotype results to json
'''
rule convert_obo2json_phenotype:
input:
- obo='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo'
+ obo='share/BioNLP-OST+EnovFood-Phenotype.obo'
output:
json='corpora/florilege/alvisir/BioNLP-OST+EnovFood-Phenotype.json'
params:
@@ -224,7 +233,7 @@ convert use results to json
'''
rule convert_obo2json_use:
input:
- obo='ancillaries/BioNLP-OST+EnovFood-Use.obo'
+ obo='share/BioNLP-OST+EnovFood-Use.obo'
output:
json='corpora/florilege/alvisir/BioNLP-OST+EnovFood-Use.json'
params:
@@ -239,9 +248,9 @@ generate concept paths
'''
rule generate_concept_path:
input:
- onto="ancillaries/{ontoname}.obo"
+ onto="share/{ontoname}.obo"
output:
- paths="ancillaries/{ontoname}.paths"
+ paths="share/{ontoname}.paths"
params:
plan="plans/get_onto_paths.plan",
tmpDir=config['TMP']
@@ -251,3 +260,7 @@ rule generate_concept_path:
-alias output {output.paths} \
{params.plan}
"""
+
+# Save timestamp
+end = time.time()
+print(end - start)
\ No newline at end of file
diff --git a/process_CIRM_corpus.snakefile b/process_CIRM_corpus.snakefile
index 87de2274fde521be29d167fae08569f213de3c9a..a18e93ac07380d29152b891c1650c100ad11a39c 100644
--- a/process_CIRM_corpus.snakefile
+++ b/process_CIRM_corpus.snakefile
@@ -162,10 +162,10 @@ rule map_cirm_habitats:
yatea_var_candidates='corpora/cirm/bia/yatea-var/candidates.xml'
params:
plan='plans/map_habitats.plan',
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
outdir='corpora/cirm/bia',
outfile='mapped_bia_habitats.txt'
singularity:config["SINGULARITY_IMG"]
@@ -190,10 +190,10 @@ rule map_cirm_yeast_habitats:
yatea_var_candidates='corpora/cirm/levures/yatea-var/candidates.xml'
params:
plan='plans/map_habitats.plan',
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
outdir='corpora/cirm/levures',
outfile='mapped_yeast_habitats.txt'
singularity:config["SINGULARITY_IMG"]
@@ -218,10 +218,10 @@ rule map_cirm_cfbp_habitats:
yatea_var_candidates='corpora/cirm/cfbp/yatea-var/candidates.xml'
params:
plan='plans/map_habitats.plan',
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
outdir='corpora/cirm/cfbp',
outfile='mapped_cfbp_habitats.txt'
singularity:config["SINGULARITY_IMG"]
diff --git a/process_DSMZ_corpus.snakefile b/process_DSMZ_corpus.snakefile
index cad248194d147eb8a05d90a6c94eb6da21c84ce5..be491094fa4df1fe6a69c2ee5a4731971c5ed9a1 100644
--- a/process_DSMZ_corpus.snakefile
+++ b/process_DSMZ_corpus.snakefile
@@ -29,7 +29,7 @@ extract dsmz sample
'''
rule extract_sample_type:
input:
- bacdive_entries='ancillaries/extended-microorganisms-taxonomy/bacdive-strains/entries'
+ bacdive_entries='share/extended-microorganisms-taxonomy/bacdive-strains/entries'
output:
'corpora/dsmz/dsmz-data/sample_type.txt'
shell: '''softwares/scripts/bacdive-extract-isolation.py {input.bacdive_entries} >{output}'''
@@ -62,10 +62,10 @@ rule map_dsmz_habitats:
params:
plan='plans/map_habitats.plan',
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
outdir='corpora/dsmz',
outfile='mapped_habitats.txt'
@@ -89,8 +89,8 @@ rule format_dsmz_results:
script='softwares/scripts/bacdive-format-results.py',
bacdive_sample_type='corpora/dsmz/dsmz-data/sample_type.txt',
mapped_habitats='corpora/dsmz/mapped_habitats.txt',
- taxids='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
- bacdive_to_taxid='ancillaries/extended-microorganisms-taxonomy/bacdive-match/bacdive-to-taxid.txt'
+ taxids='share/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ bacdive_to_taxid='share/extended-microorganisms-taxonomy/bacdive-match/bacdive-to-taxid.txt'
output:
result='corpora/florilege/dsmz/dsmz-results.txt',
diff --git a/process_GenBank_corpus.snakefile b/process_GenBank_corpus.snakefile
index 7c4d712565985aec1bd5117a96ba1f59e8386659..b83d45a7506d8c53eeccfc30f4fa0c683f2dff77 100644
--- a/process_GenBank_corpus.snakefile
+++ b/process_GenBank_corpus.snakefile
@@ -87,10 +87,10 @@ rule map_genbank_habitats:
mapped_habitats='corpora/genbank/mapped_habitats.txt'
params:
plan='plans/map_habitats.plan',
- onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
+ onto='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
outdir='corpora/genbank',
outfile='mapped_habitats.txt'
singularity:config["SINGULARITY_IMG"]
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 14d19ee940569ff076dfcb9312fff8b5f794f5cc..8d2d5b486f405e396eeb960a263486949fb5a72d 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -60,13 +60,13 @@ rule run_pubmed_main:
params:
batch="{B}",
corpus='pubmed',
- onto_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
- tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
- onto_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
- tomap_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
- graylist='ancillaries/graylist_extended.heads',
- emptywords='ancillaries/stopwords_EN.ttg',
- onto_use='ancillaries/BioNLP-OST+EnovFood-Use.obo',
+ onto_habitat='share/BioNLP-OST+EnovFood-Habitat.obo',
+ tomap_habitat='share/BioNLP-OST+EnovFood-Habitat.tomap',
+ onto_pheno='share/BioNLP-OST+EnovFood-Phenotype.obo',
+ tomap_pheno='share/BioNLP-OST+EnovFood-Phenotype.tomap',
+ graylist='share/graylist_extended.heads',
+ emptywords='share/stopwords_EN.ttg',
+ onto_use='share/BioNLP-OST+EnovFood-Use.obo',
plan='plans/omnicrobe_main.plan',
dir=config["PUBMED_BATCHES_HOME"] + "/{B}/",
taxid_microorganisms=config['NCBI_TAXO_MICROORGANISMS'],
@@ -166,11 +166,11 @@ create the expander
'''
rule create_pubmed_expander:
input:
- expander="ancillaries/expander.xml",
+ expander="share/expander.xml",
taxa_id_microorganisms=config['NCBI_TAXO_AND_ID_MICROORGANISMS'],
- onto_habitat="ancillaries/BioNLP-OST+EnovFood-Habitat.obo",
- onto_phenotype="ancillaries/BioNLP-OST+EnovFood-Phenotype.obo",
- onto_use="ancillaries/BioNLP-OST+EnovFood-Use.obo"
+ onto_habitat="share/BioNLP-OST+EnovFood-Habitat.obo",
+ onto_phenotype="share/BioNLP-OST+EnovFood-Phenotype.obo",
+ onto_use="share/BioNLP-OST+EnovFood-Use.obo"
output:
expander_folder=directory("corpora/florilege/alvisir/expander")
params:
diff --git a/ancillaries/2017MeshTree.txt b/share/2017MeshTree.txt
similarity index 100%
rename from ancillaries/2017MeshTree.txt
rename to share/2017MeshTree.txt
diff --git a/ancillaries/BioNLP-OST+EnovFood.obo b/share/BioNLP-OST+EnovFood.obo
similarity index 100%
rename from ancillaries/BioNLP-OST+EnovFood.obo
rename to share/BioNLP-OST+EnovFood.obo
diff --git a/ancillaries/CCG/models/parser/cats/markedup b/share/CCG/models/parser/cats/markedup
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/markedup
rename to share/CCG/models/parser/cats/markedup
diff --git a/ancillaries/CCG/models/parser/cats/markedup_sd-1.00 b/share/CCG/models/parser/cats/markedup_sd-1.00
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/markedup_sd-1.00
rename to share/CCG/models/parser/cats/markedup_sd-1.00
diff --git a/ancillaries/CCG/models/parser/cats/trAP b/share/CCG/models/parser/cats/trAP
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/trAP
rename to share/CCG/models/parser/cats/trAP
diff --git a/ancillaries/CCG/models/parser/cats/trNP b/share/CCG/models/parser/cats/trNP
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/trNP
rename to share/CCG/models/parser/cats/trNP
diff --git a/ancillaries/CCG/models/parser/cats/trPP b/share/CCG/models/parser/cats/trPP
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/trPP
rename to share/CCG/models/parser/cats/trPP
diff --git a/ancillaries/CCG/models/parser/cats/trPP_qus b/share/CCG/models/parser/cats/trPP_qus
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/trPP_qus
rename to share/CCG/models/parser/cats/trPP_qus
diff --git a/ancillaries/CCG/models/parser/cats/trVP_to b/share/CCG/models/parser/cats/trVP_to
similarity index 100%
rename from ancillaries/CCG/models/parser/cats/trVP_to
rename to share/CCG/models/parser/cats/trVP_to
diff --git a/ancillaries/CCG/models/parser/config b/share/CCG/models/parser/config
similarity index 100%
rename from ancillaries/CCG/models/parser/config
rename to share/CCG/models/parser/config
diff --git a/ancillaries/CCG/models/parser/features b/share/CCG/models/parser/features
similarity index 100%
rename from ancillaries/CCG/models/parser/features
rename to share/CCG/models/parser/features
diff --git a/ancillaries/CCG/models/parser/info b/share/CCG/models/parser/info
similarity index 100%
rename from ancillaries/CCG/models/parser/info
rename to share/CCG/models/parser/info
diff --git a/ancillaries/CCG/models/parser/lexicon b/share/CCG/models/parser/lexicon
similarity index 100%
rename from ancillaries/CCG/models/parser/lexicon
rename to share/CCG/models/parser/lexicon
diff --git a/ancillaries/CCG/models/parser/log b/share/CCG/models/parser/log
similarity index 100%
rename from ancillaries/CCG/models/parser/log
rename to share/CCG/models/parser/log
diff --git a/ancillaries/CCG/models/parser/model.config b/share/CCG/models/parser/model.config
similarity index 100%
rename from ancillaries/CCG/models/parser/model.config
rename to share/CCG/models/parser/model.config
diff --git a/ancillaries/CCG/models/parser/rules b/share/CCG/models/parser/rules
similarity index 100%
rename from ancillaries/CCG/models/parser/rules
rename to share/CCG/models/parser/rules
diff --git a/ancillaries/CCG/models/parser/stats b/share/CCG/models/parser/stats
similarity index 100%
rename from ancillaries/CCG/models/parser/stats
rename to share/CCG/models/parser/stats
diff --git a/ancillaries/CCG/models/parser/weights b/share/CCG/models/parser/weights
similarity index 100%
rename from ancillaries/CCG/models/parser/weights
rename to share/CCG/models/parser/weights
diff --git a/ancillaries/CCG/models/pos_bio-1.00/attributes b/share/CCG/models/pos_bio-1.00/attributes
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/attributes
rename to share/CCG/models/pos_bio-1.00/attributes
diff --git a/ancillaries/CCG/models/pos_bio-1.00/classes b/share/CCG/models/pos_bio-1.00/classes
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/classes
rename to share/CCG/models/pos_bio-1.00/classes
diff --git a/ancillaries/CCG/models/pos_bio-1.00/config b/share/CCG/models/pos_bio-1.00/config
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/config
rename to share/CCG/models/pos_bio-1.00/config
diff --git a/ancillaries/CCG/models/pos_bio-1.00/contexts b/share/CCG/models/pos_bio-1.00/contexts
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/contexts
rename to share/CCG/models/pos_bio-1.00/contexts
diff --git a/ancillaries/CCG/models/pos_bio-1.00/features b/share/CCG/models/pos_bio-1.00/features
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/features
rename to share/CCG/models/pos_bio-1.00/features
diff --git a/ancillaries/CCG/models/pos_bio-1.00/info b/share/CCG/models/pos_bio-1.00/info
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/info
rename to share/CCG/models/pos_bio-1.00/info
diff --git a/ancillaries/CCG/models/pos_bio-1.00/lexicon b/share/CCG/models/pos_bio-1.00/lexicon
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/lexicon
rename to share/CCG/models/pos_bio-1.00/lexicon
diff --git a/ancillaries/CCG/models/pos_bio-1.00/number_unknowns b/share/CCG/models/pos_bio-1.00/number_unknowns
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/number_unknowns
rename to share/CCG/models/pos_bio-1.00/number_unknowns
diff --git a/ancillaries/CCG/models/pos_bio-1.00/tagdict b/share/CCG/models/pos_bio-1.00/tagdict
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/tagdict
rename to share/CCG/models/pos_bio-1.00/tagdict
diff --git a/ancillaries/CCG/models/pos_bio-1.00/unknowns b/share/CCG/models/pos_bio-1.00/unknowns
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/unknowns
rename to share/CCG/models/pos_bio-1.00/unknowns
diff --git a/ancillaries/CCG/models/pos_bio-1.00/weights b/share/CCG/models/pos_bio-1.00/weights
similarity index 100%
rename from ancillaries/CCG/models/pos_bio-1.00/weights
rename to share/CCG/models/pos_bio-1.00/weights
diff --git a/ancillaries/CCG/models/super_bio-1.00/attributes b/share/CCG/models/super_bio-1.00/attributes
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/attributes
rename to share/CCG/models/super_bio-1.00/attributes
diff --git a/ancillaries/CCG/models/super_bio-1.00/classes b/share/CCG/models/super_bio-1.00/classes
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/classes
rename to share/CCG/models/super_bio-1.00/classes
diff --git a/ancillaries/CCG/models/super_bio-1.00/config b/share/CCG/models/super_bio-1.00/config
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/config
rename to share/CCG/models/super_bio-1.00/config
diff --git a/ancillaries/CCG/models/super_bio-1.00/contexts b/share/CCG/models/super_bio-1.00/contexts
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/contexts
rename to share/CCG/models/super_bio-1.00/contexts
diff --git a/ancillaries/CCG/models/super_bio-1.00/features b/share/CCG/models/super_bio-1.00/features
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/features
rename to share/CCG/models/super_bio-1.00/features
diff --git a/ancillaries/CCG/models/super_bio-1.00/info b/share/CCG/models/super_bio-1.00/info
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/info
rename to share/CCG/models/super_bio-1.00/info
diff --git a/ancillaries/CCG/models/super_bio-1.00/lexicon b/share/CCG/models/super_bio-1.00/lexicon
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/lexicon
rename to share/CCG/models/super_bio-1.00/lexicon
diff --git a/ancillaries/CCG/models/super_bio-1.00/posdict b/share/CCG/models/super_bio-1.00/posdict
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/posdict
rename to share/CCG/models/super_bio-1.00/posdict
diff --git a/ancillaries/CCG/models/super_bio-1.00/postags b/share/CCG/models/super_bio-1.00/postags
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/postags
rename to share/CCG/models/super_bio-1.00/postags
diff --git a/ancillaries/CCG/models/super_bio-1.00/tagdict b/share/CCG/models/super_bio-1.00/tagdict
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/tagdict
rename to share/CCG/models/super_bio-1.00/tagdict
diff --git a/ancillaries/CCG/models/super_bio-1.00/unknowns b/share/CCG/models/super_bio-1.00/unknowns
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/unknowns
rename to share/CCG/models/super_bio-1.00/unknowns
diff --git a/ancillaries/CCG/models/super_bio-1.00/weights b/share/CCG/models/super_bio-1.00/weights
similarity index 100%
rename from ancillaries/CCG/models/super_bio-1.00/weights
rename to share/CCG/models/super_bio-1.00/weights
diff --git a/ancillaries/Florilege/DB/CIRM/2019-07-05/extraction_3-fv.csv b/share/Florilege/DB/CIRM/2019-07-05/extraction_3-fv.csv
similarity index 100%
rename from ancillaries/Florilege/DB/CIRM/2019-07-05/extraction_3-fv.csv
rename to share/Florilege/DB/CIRM/2019-07-05/extraction_3-fv.csv
diff --git a/ancillaries/Florilege/DB/GenBank/req1_sup800_bacteria-descriptors.csv b/share/Florilege/DB/GenBank/req1_sup800_bacteria-descriptors.csv
similarity index 100%
rename from ancillaries/Florilege/DB/GenBank/req1_sup800_bacteria-descriptors.csv
rename to share/Florilege/DB/GenBank/req1_sup800_bacteria-descriptors.csv
diff --git a/ancillaries/YaTeA/config-habitats/EN/ChunkingExceptions b/share/YaTeA/config-habitats/EN/ChunkingExceptions
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/ChunkingExceptions
rename to share/YaTeA/config-habitats/EN/ChunkingExceptions
diff --git a/ancillaries/YaTeA/config-habitats/EN/ChunkingFrontiers b/share/YaTeA/config-habitats/EN/ChunkingFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/ChunkingFrontiers
rename to share/YaTeA/config-habitats/EN/ChunkingFrontiers
diff --git a/ancillaries/YaTeA/config-habitats/EN/CleaningExceptions b/share/YaTeA/config-habitats/EN/CleaningExceptions
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/CleaningExceptions
rename to share/YaTeA/config-habitats/EN/CleaningExceptions
diff --git a/ancillaries/YaTeA/config-habitats/EN/CleaningFrontiers b/share/YaTeA/config-habitats/EN/CleaningFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/CleaningFrontiers
rename to share/YaTeA/config-habitats/EN/CleaningFrontiers
diff --git a/ancillaries/YaTeA/config-habitats/EN/ForbiddenStructures b/share/YaTeA/config-habitats/EN/ForbiddenStructures
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/ForbiddenStructures
rename to share/YaTeA/config-habitats/EN/ForbiddenStructures
diff --git a/ancillaries/YaTeA/config-habitats/EN/LGPmapping b/share/YaTeA/config-habitats/EN/LGPmapping
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/LGPmapping
rename to share/YaTeA/config-habitats/EN/LGPmapping
diff --git a/ancillaries/YaTeA/config-habitats/EN/LinguisticConfiguration b/share/YaTeA/config-habitats/EN/LinguisticConfiguration
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/LinguisticConfiguration
rename to share/YaTeA/config-habitats/EN/LinguisticConfiguration
diff --git a/ancillaries/YaTeA/config-habitats/EN/Options b/share/YaTeA/config-habitats/EN/Options
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/Options
rename to share/YaTeA/config-habitats/EN/Options
diff --git a/ancillaries/YaTeA/config-habitats/EN/ParsingPatterns b/share/YaTeA/config-habitats/EN/ParsingPatterns
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/ParsingPatterns
rename to share/YaTeA/config-habitats/EN/ParsingPatterns
diff --git a/ancillaries/YaTeA/config-habitats/EN/TagSet b/share/YaTeA/config-habitats/EN/TagSet
similarity index 100%
rename from ancillaries/YaTeA/config-habitats/EN/TagSet
rename to share/YaTeA/config-habitats/EN/TagSet
diff --git a/ancillaries/YaTeA/config/EN/ChunkingExceptions b/share/YaTeA/config/EN/ChunkingExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/EN/ChunkingExceptions
rename to share/YaTeA/config/EN/ChunkingExceptions
diff --git a/ancillaries/YaTeA/config/EN/ChunkingFrontiers b/share/YaTeA/config/EN/ChunkingFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/EN/ChunkingFrontiers
rename to share/YaTeA/config/EN/ChunkingFrontiers
diff --git a/ancillaries/YaTeA/config/EN/CleaningExceptions b/share/YaTeA/config/EN/CleaningExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/EN/CleaningExceptions
rename to share/YaTeA/config/EN/CleaningExceptions
diff --git a/ancillaries/YaTeA/config/EN/CleaningFrontiers b/share/YaTeA/config/EN/CleaningFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/EN/CleaningFrontiers
rename to share/YaTeA/config/EN/CleaningFrontiers
diff --git a/ancillaries/YaTeA/config/EN/ForbiddenStructures b/share/YaTeA/config/EN/ForbiddenStructures
similarity index 100%
rename from ancillaries/YaTeA/config/EN/ForbiddenStructures
rename to share/YaTeA/config/EN/ForbiddenStructures
diff --git a/ancillaries/YaTeA/config/EN/LGPmapping b/share/YaTeA/config/EN/LGPmapping
similarity index 100%
rename from ancillaries/YaTeA/config/EN/LGPmapping
rename to share/YaTeA/config/EN/LGPmapping
diff --git a/ancillaries/YaTeA/config/EN/Options b/share/YaTeA/config/EN/Options
similarity index 100%
rename from ancillaries/YaTeA/config/EN/Options
rename to share/YaTeA/config/EN/Options
diff --git a/ancillaries/YaTeA/config/EN/ParsingPatterns b/share/YaTeA/config/EN/ParsingPatterns
similarity index 100%
rename from ancillaries/YaTeA/config/EN/ParsingPatterns
rename to share/YaTeA/config/EN/ParsingPatterns
diff --git a/ancillaries/YaTeA/config/EN/TagSet b/share/YaTeA/config/EN/TagSet
similarity index 100%
rename from ancillaries/YaTeA/config/EN/TagSet
rename to share/YaTeA/config/EN/TagSet
diff --git a/ancillaries/YaTeA/config/FR-Flemm/ChunkingExceptions b/share/YaTeA/config/FR-Flemm/ChunkingExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/ChunkingExceptions
rename to share/YaTeA/config/FR-Flemm/ChunkingExceptions
diff --git a/ancillaries/YaTeA/config/FR-Flemm/ChunkingFrontiers b/share/YaTeA/config/FR-Flemm/ChunkingFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/ChunkingFrontiers
rename to share/YaTeA/config/FR-Flemm/ChunkingFrontiers
diff --git a/ancillaries/YaTeA/config/FR-Flemm/CleaningExceptions b/share/YaTeA/config/FR-Flemm/CleaningExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/CleaningExceptions
rename to share/YaTeA/config/FR-Flemm/CleaningExceptions
diff --git a/ancillaries/YaTeA/config/FR-Flemm/CleaningFrontiers b/share/YaTeA/config/FR-Flemm/CleaningFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/CleaningFrontiers
rename to share/YaTeA/config/FR-Flemm/CleaningFrontiers
diff --git a/ancillaries/YaTeA/config/FR-Flemm/ForbiddenStructures b/share/YaTeA/config/FR-Flemm/ForbiddenStructures
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/ForbiddenStructures
rename to share/YaTeA/config/FR-Flemm/ForbiddenStructures
diff --git a/ancillaries/YaTeA/config/FR-Flemm/Options b/share/YaTeA/config/FR-Flemm/Options
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/Options
rename to share/YaTeA/config/FR-Flemm/Options
diff --git a/ancillaries/YaTeA/config/FR-Flemm/ParsingPatterns b/share/YaTeA/config/FR-Flemm/ParsingPatterns
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/ParsingPatterns
rename to share/YaTeA/config/FR-Flemm/ParsingPatterns
diff --git a/ancillaries/YaTeA/config/FR-Flemm/TagSet b/share/YaTeA/config/FR-Flemm/TagSet
similarity index 100%
rename from ancillaries/YaTeA/config/FR-Flemm/TagSet
rename to share/YaTeA/config/FR-Flemm/TagSet
diff --git a/ancillaries/YaTeA/config/FR/ChunkingExceptions b/share/YaTeA/config/FR/ChunkingExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/FR/ChunkingExceptions
rename to share/YaTeA/config/FR/ChunkingExceptions
diff --git a/ancillaries/YaTeA/config/FR/ChunkingFrontiers b/share/YaTeA/config/FR/ChunkingFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/FR/ChunkingFrontiers
rename to share/YaTeA/config/FR/ChunkingFrontiers
diff --git a/ancillaries/YaTeA/config/FR/CleaningExceptions b/share/YaTeA/config/FR/CleaningExceptions
similarity index 100%
rename from ancillaries/YaTeA/config/FR/CleaningExceptions
rename to share/YaTeA/config/FR/CleaningExceptions
diff --git a/ancillaries/YaTeA/config/FR/CleaningFrontiers b/share/YaTeA/config/FR/CleaningFrontiers
similarity index 100%
rename from ancillaries/YaTeA/config/FR/CleaningFrontiers
rename to share/YaTeA/config/FR/CleaningFrontiers
diff --git a/ancillaries/YaTeA/config/FR/CoordPatterns b/share/YaTeA/config/FR/CoordPatterns
similarity index 100%
rename from ancillaries/YaTeA/config/FR/CoordPatterns
rename to share/YaTeA/config/FR/CoordPatterns
diff --git a/ancillaries/YaTeA/config/FR/ForbiddenStructures b/share/YaTeA/config/FR/ForbiddenStructures
similarity index 100%
rename from ancillaries/YaTeA/config/FR/ForbiddenStructures
rename to share/YaTeA/config/FR/ForbiddenStructures
diff --git a/ancillaries/YaTeA/config/FR/LinguisticConfiguration b/share/YaTeA/config/FR/LinguisticConfiguration
similarity index 100%
rename from ancillaries/YaTeA/config/FR/LinguisticConfiguration
rename to share/YaTeA/config/FR/LinguisticConfiguration
diff --git a/ancillaries/YaTeA/config/FR/Options b/share/YaTeA/config/FR/Options
similarity index 100%
rename from ancillaries/YaTeA/config/FR/Options
rename to share/YaTeA/config/FR/Options
diff --git a/ancillaries/YaTeA/config/FR/ParsingPatterns b/share/YaTeA/config/FR/ParsingPatterns
similarity index 100%
rename from ancillaries/YaTeA/config/FR/ParsingPatterns
rename to share/YaTeA/config/FR/ParsingPatterns
diff --git a/ancillaries/YaTeA/config/FR/TagSet b/share/YaTeA/config/FR/TagSet
similarity index 100%
rename from ancillaries/YaTeA/config/FR/TagSet
rename to share/YaTeA/config/FR/TagSet
diff --git a/ancillaries/YaTeA/config/FR/mapping.TT2Lexter b/share/YaTeA/config/FR/mapping.TT2Lexter
similarity index 100%
rename from ancillaries/YaTeA/config/FR/mapping.TT2Lexter
rename to share/YaTeA/config/FR/mapping.TT2Lexter
diff --git a/ancillaries/YaTeA/locale/EN/Messages b/share/YaTeA/locale/EN/Messages
similarity index 100%
rename from ancillaries/YaTeA/locale/EN/Messages
rename to share/YaTeA/locale/EN/Messages
diff --git a/ancillaries/YaTeA/locale/FR/Messages b/share/YaTeA/locale/FR/Messages
similarity index 100%
rename from ancillaries/YaTeA/locale/FR/Messages
rename to share/YaTeA/locale/FR/Messages
diff --git a/ancillaries/YaTeA/samples/bootstrap.testified b/share/YaTeA/samples/bootstrap.testified
similarity index 100%
rename from ancillaries/YaTeA/samples/bootstrap.testified
rename to share/YaTeA/samples/bootstrap.testified
diff --git a/ancillaries/YaTeA/samples/corpus.ttg b/share/YaTeA/samples/corpus.ttg
similarity index 100%
rename from ancillaries/YaTeA/samples/corpus.ttg
rename to share/YaTeA/samples/corpus.ttg
diff --git a/ancillaries/YaTeA/samples/environment_EN.TT b/share/YaTeA/samples/environment_EN.TT
similarity index 100%
rename from ancillaries/YaTeA/samples/environment_EN.TT
rename to share/YaTeA/samples/environment_EN.TT
diff --git a/ancillaries/YaTeA/samples/pmid10788508-v2.1l b/share/YaTeA/samples/pmid10788508-v2.1l
similarity index 100%
rename from ancillaries/YaTeA/samples/pmid10788508-v2.1l
rename to share/YaTeA/samples/pmid10788508-v2.1l
diff --git a/ancillaries/YaTeA/samples/pmid10788508-v2.TT b/share/YaTeA/samples/pmid10788508-v2.TT
similarity index 100%
rename from ancillaries/YaTeA/samples/pmid10788508-v2.TT
rename to share/YaTeA/samples/pmid10788508-v2.TT
diff --git a/ancillaries/YaTeA/samples/sampleEN.ttg b/share/YaTeA/samples/sampleEN.ttg
similarity index 100%
rename from ancillaries/YaTeA/samples/sampleEN.ttg
rename to share/YaTeA/samples/sampleEN.ttg
diff --git a/ancillaries/YaTeA/samples/termes_environnement.ttg b/share/YaTeA/samples/termes_environnement.ttg
similarity index 100%
rename from ancillaries/YaTeA/samples/termes_environnement.ttg
rename to share/YaTeA/samples/termes_environnement.ttg
diff --git a/ancillaries/YaTeA/samples/termes_environnement.txt b/share/YaTeA/samples/termes_environnement.txt
similarity index 100%
rename from ancillaries/YaTeA/samples/termes_environnement.txt
rename to share/YaTeA/samples/termes_environnement.txt
diff --git a/ancillaries/YaTeA/samples/termlist b/share/YaTeA/samples/termlist
similarity index 100%
rename from ancillaries/YaTeA/samples/termlist
rename to share/YaTeA/samples/termlist
diff --git a/ancillaries/YaTeA/samples/termlist.TT b/share/YaTeA/samples/termlist.TT
similarity index 100%
rename from ancillaries/YaTeA/samples/termlist.TT
rename to share/YaTeA/samples/termlist.TT
diff --git a/ancillaries/YaTeA/samples/termsEnvironment.ttg b/share/YaTeA/samples/termsEnvironment.ttg
similarity index 100%
rename from ancillaries/YaTeA/samples/termsEnvironment.ttg
rename to share/YaTeA/samples/termsEnvironment.ttg
diff --git a/ancillaries/YaTeA/samples/termsEnvironment.txt b/share/YaTeA/samples/termsEnvironment.txt
similarity index 100%
rename from ancillaries/YaTeA/samples/termsEnvironment.txt
rename to share/YaTeA/samples/termsEnvironment.txt
diff --git a/ancillaries/YaTeA/samples/termsPhB.termsgt b/share/YaTeA/samples/termsPhB.termsgt
similarity index 100%
rename from ancillaries/YaTeA/samples/termsPhB.termsgt
rename to share/YaTeA/samples/termsPhB.termsgt
diff --git a/ancillaries/YaTeA/samples/transcript-epure-Genia.bootstrap b/share/YaTeA/samples/transcript-epure-Genia.bootstrap
similarity index 100%
rename from ancillaries/YaTeA/samples/transcript-epure-Genia.bootstrap
rename to share/YaTeA/samples/transcript-epure-Genia.bootstrap
diff --git a/ancillaries/YaTeA/yatea.conf b/share/YaTeA/yatea.conf
similarity index 100%
rename from ancillaries/YaTeA/yatea.conf
rename to share/YaTeA/yatea.conf
diff --git a/ancillaries/YaTeA/yatea.rc b/share/YaTeA/yatea.rc
similarity index 100%
rename from ancillaries/YaTeA/yatea.rc
rename to share/YaTeA/yatea.rc
diff --git a/ancillaries/anaphoraLexicon.txt b/share/anaphoraLexicon.txt
similarity index 100%
rename from ancillaries/anaphoraLexicon.txt
rename to share/anaphoraLexicon.txt
diff --git a/ancillaries/biAnaphoraLexicon.txt b/share/biAnaphoraLexicon.txt
similarity index 100%
rename from ancillaries/biAnaphoraLexicon.txt
rename to share/biAnaphoraLexicon.txt
diff --git a/ancillaries/blacklist.txt b/share/blacklist.txt
similarity index 100%
rename from ancillaries/blacklist.txt
rename to share/blacklist.txt
diff --git a/ancillaries/blacklisted-heads.txt b/share/blacklisted-heads.txt
similarity index 100%
rename from ancillaries/blacklisted-heads.txt
rename to share/blacklisted-heads.txt
diff --git a/ancillaries/blacklisted-phenotype-heads.txt b/share/blacklisted-phenotype-heads.txt
similarity index 100%
rename from ancillaries/blacklisted-phenotype-heads.txt
rename to share/blacklisted-phenotype-heads.txt
diff --git a/ancillaries/default-taxon-disambiguation.txt b/share/default-taxon-disambiguation.txt
similarity index 100%
rename from ancillaries/default-taxon-disambiguation.txt
rename to share/default-taxon-disambiguation.txt
diff --git a/ancillaries/expander.xml b/share/expander.xml
similarity index 100%
rename from ancillaries/expander.xml
rename to share/expander.xml
diff --git a/ancillaries/graylist_extended.heads b/share/graylist_extended.heads
similarity index 100%
rename from ancillaries/graylist_extended.heads
rename to share/graylist_extended.heads
diff --git a/ancillaries/microbes-2019-pubmed2alvisnlp.xslt b/share/microbes-2019-pubmed2alvisnlp.xslt
similarity index 100%
rename from ancillaries/microbes-2019-pubmed2alvisnlp.xslt
rename to share/microbes-2019-pubmed2alvisnlp.xslt
diff --git a/ancillaries/microorganism_stopwords.txt b/share/microorganism_stopwords.txt
similarity index 100%
rename from ancillaries/microorganism_stopwords.txt
rename to share/microorganism_stopwords.txt
diff --git a/ancillaries/not-trees.txt b/share/not-trees.txt
similarity index 100%
rename from ancillaries/not-trees.txt
rename to share/not-trees.txt
diff --git a/ancillaries/not-walls.txt b/share/not-walls.txt
similarity index 100%
rename from ancillaries/not-walls.txt
rename to share/not-walls.txt
diff --git a/ancillaries/noun_adj_and_spelling_variants b/share/noun_adj_and_spelling_variants
similarity index 100%
rename from ancillaries/noun_adj_and_spelling_variants
rename to share/noun_adj_and_spelling_variants
diff --git a/ancillaries/phenotype_blacklist.txt b/share/phenotype_blacklist.txt
similarity index 100%
rename from ancillaries/phenotype_blacklist.txt
rename to share/phenotype_blacklist.txt
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz b/share/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz
rename to share/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.crf.ser.gz
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.prop b/share/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.prop
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.prop
rename to share/stanford-ner-2014-06-16/classifiers/english.all.3class.distsim.prop
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.crf.ser.gz b/share/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.crf.ser.gz
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.crf.ser.gz
rename to share/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.crf.ser.gz
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.prop b/share/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.prop
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.prop
rename to share/stanford-ner-2014-06-16/classifiers/english.conll.4class.distsim.prop
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.crf.ser.gz b/share/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.crf.ser.gz
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.crf.ser.gz
rename to share/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.crf.ser.gz
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.prop b/share/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.prop
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.prop
rename to share/stanford-ner-2014-06-16/classifiers/english.muc.7class.distsim.prop
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.crf.ser.gz b/share/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.crf.ser.gz
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.crf.ser.gz
rename to share/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.crf.ser.gz
diff --git a/ancillaries/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.prop b/share/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.prop
similarity index 100%
rename from ancillaries/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.prop
rename to share/stanford-ner-2014-06-16/classifiers/english.nowiki.3class.distsim.prop
diff --git a/ancillaries/stopwords_EN.ttg b/share/stopwords_EN.ttg
similarity index 100%
rename from ancillaries/stopwords_EN.ttg
rename to share/stopwords_EN.ttg
diff --git a/ancillaries/stopwords_EN.txt b/share/stopwords_EN.txt
similarity index 100%
rename from ancillaries/stopwords_EN.txt
rename to share/stopwords_EN.txt
diff --git a/update_microbio_corpus.snakefile b/update_microbio_corpus.snakefile
index 66d06e41a1fb8e4c6fa18d1b79f6597afd9e52c5..33c589bbdf944fd388a5c5821878f1c02ed7ed4e 100644
--- a/update_microbio_corpus.snakefile
+++ b/update_microbio_corpus.snakefile
@@ -7,8 +7,9 @@ all
'''
rule all:
input:
- corpus=directory("corpora/pubmed/batches"),
- meta="corpora/pubmed/info.csv"
+ corpus="corpora/pubmed/batches",
+ pmcid_file = "corpora/epmc/pmcids.full.txt",
+ meta = "corpora/pubmed/info.csv"
'''
@@ -26,6 +27,93 @@ rule generate_corpora:
softwares/java-utils/bin/pubmed-search -index {input.db} -outdir {output.corpus} -xml %%/batch.xml -pmid %%/pmids.txt -mesh-tree-query {params.request} -batch 100
"""
+
+BATCHES, = glob_wildcards("corpora/pubmed/batches/{id}/pmids.txt")
+'''
+get pmcids for each batch
+'''
+rule get_PMCID:
+ input:
+ corpus = "corpora/pubmed/batches",
+ pmid_file = "corpora/pubmed/batches/{B}/pmids.txt"
+ output:
+ pmcid_file = "corpora/epmc/pmcids/{B}/pmcids.txt"
+ params:
+ request_root = config["PMC_REQUEST_ROOT"]
+ run:
+ import io
+ import os
+ import requests
+ from requests.structures import CaseInsensitiveDict
+ from requests.utils import requote_uri
+ import pandas
+ import json
+ df = pandas.read_csv(input.pmid_file, names = ['pmid'])
+ RQT_OPS = '%20OR%20EXT_ID:'.join(list(map(str, df.pmid)))
+ request = params.request_root + "search?query=(" + RQT_OPS + ")"
+ request = request + "%20AND%20SRC:MED%20AND%20OPEN_ACCESS:y&resultType=idlist"
+ headers = CaseInsensitiveDict()
+ headers["accept"] = "application/json"
+ resp = requests.get(request, headers=headers)
+ binary = resp.content
+ Jdata = json.loads(binary)
+ Jlist = Jdata["resultList"]["result"]
+ pmcids = [e['pmcid'] for e in Jlist if 'pmcid' in e.keys()]
+ pandas.DataFrame(pmcids).to_csv(output.pmcid_file, index=False)
+
+
+'''
+get fulltexts for each batch
+'''
+rule get_XML:
+ input:
+ pmcid_file = "corpora/epmc/pmcids/{B}/pmcids.txt"
+ output:
+ corpus_folder = directory("corpora/epmc/batches/{B}/")
+ params:
+ request_root = config["PMC_REQUEST_ROOT"]
+ run:
+ import os
+ import io
+ import requests
+ from requests.structures import CaseInsensitiveDict
+ from requests.utils import requote_uri
+ import pandas
+ import json
+ df = pandas.read_csv(input.pmcid_file, names = ['pmcid'])
+ data = []
+ for index, row in df.iterrows():
+ pmcid = row["pmcid"]
+ request = params.request_root
+ request = request + pmcid
+ request = request + "/fullTextXML"
+ headers = CaseInsensitiveDict()
+ headers["accept"] = "application/xml"
+ resp = requests.get(request, headers=headers)
+ filename = output.corpus_folder + '/'+ pmcid + '.xml'
+ os.makedirs(os.path.dirname(filename), exist_ok=True)
+ with open(filename, 'w+') as f:
+ f.write(resp.text)
+
+
+'''
+'''
+rule merge:
+ input:
+ batch_folder=expand("corpora/epmc/batches/{B}/", B=BATCHES)
+ output:
+ pmcid_file="corpora/epmc/pmcids.full.txt"
+ params:
+ pmcid_file = "pmcids.txt"
+ run:
+ pf = input.batch_folder + params.pmcid_file
+ with open(output.pmcid_file, 'w') as out:
+ for fname in pf:
+ with open(fname) as infile:
+ out.write(infile.read())
+
+
+
'''
get metadata
'''