From 68c762debc4008f7ea03b6f46091c7d0830564f8 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 14:36:30 +0000
Subject: [PATCH 01/21] Update corpora/florilege/labels.stats
---
corpora/florilege/labels.stats | 21 ++++++++++++---------
1 file changed, 12 insertions(+), 9 deletions(-)
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index b3c55895..2506702e 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1,18 +1,21 @@
id,libelle,uri
-cirm_000, date de mise à jour des données de cirm, /db/maj/genbank/date
+cirm_000, date de mise à jour des données cirm, /db/maj/genbank/date
cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
-cirm_002,nombre d'entrées cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
-cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_taxids.txt
+cirm_002,nombre d'entrées de cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
+cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_bia_taxa.txt
cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
-cirm_006,nombre d'habitat de cirm-Levure,cirm/mapped_yeast_habitats.txt
-genbank_000, date de mise à jour des données de genbank,/db/maj/genbank/date
+cirm_006,nombre d'habitats de cirm-Levure,cirm/mapped_yeast_habitats.txt
+cirm_007,nombre d'entrées de cirm-cfpb,corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
+cirm_006,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
+cirm_006,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
+genbank_000, date de mise à jour des données genbank,/db/maj/genbank/date
genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
-genbank_002,nombre de taxon de genbank,genbank/mapped_taxids.txt
+genbank_002,nombre de taxons de genbank,genbank/mapped_taxa.txt
genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
dsmz_000, date de mise à jour des données de dsmz,/db/maj/dsmz/date
dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
-dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
+dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxa.txt
dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
@@ -28,9 +31,9 @@ eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
eval_002, date d'évaluation, migale/evaluation/BB19/date
eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
+eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
+eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
eval_BB19-rel+ner_002, score global sur la prédiction de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Standard_scoring
eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
--
GitLab
From 03d3b7c1f4c289fae6e00337e193e7c642171aaf Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 14:43:29 +0000
Subject: [PATCH 02/21] Update corpora/florilege/labels.stats Deleted
corpora/florilege/stats.labels
---
corpora/florilege/labels.stats | 11 +++++------
corpora/florilege/stats.labels | 22 ----------------------
2 files changed, 5 insertions(+), 28 deletions(-)
delete mode 100644 corpora/florilege/stats.labels
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 2506702e..9082013d 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -21,12 +21,11 @@ pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
-pubmed_004,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
-pubmed_005,nombre de relations du type #Phenotype-Relations pubmed,microbes-2019/phenotype-relations.txt
-pubmed_006,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
-pubmed_007,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
-pubmed_008,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
-pubmed_009,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
+pubmed_004,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
+pubmed_005,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
+pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/habitat-relations.full.txt
+pubmed_007,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
+pubmed_008,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
eval_002, date d'évaluation, migale/evaluation/BB19/date
eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
diff --git a/corpora/florilege/stats.labels b/corpora/florilege/stats.labels
deleted file mode 100644
index 3be2a540..00000000
--- a/corpora/florilege/stats.labels
+++ /dev/null
@@ -1,22 +0,0 @@
-LIBELLE,file
-entrées cirm,cirm/2019-07-05/extraction_3-fv.csv
-entrées cirm (levure),cirm/Levures_2017/data_CIRM_levures_extraction_09032017.csv
-taxid cirm,cirm/mapped_taxids.txt
-yeast cirm,cirm/yeast_taxa.txt
-habitats cirm,cirm/mapped_habitats.txt
-habitats cirm (yeast),cirm/mapped_yeast_habitats.txt
-entrées genbank,genbank/req1_sup800_bacteria-descriptors.csv
-taxid genbank,genbank/mapped_taxids.txt
-habitats genbank,genbank/mapped_habitats.txt
-entrées dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
-taxid dsmz,dsmz/mapped_taxids.txt
-habitats dsmz,dsmz/mapped_habitats.txt
-batch (x1000) pubmed,microbes-2019/list_of_batches.txt
-habitats pubmed,microbes-2019/habitats.full.txt
-microorganisms pubmed,microbes-2019/microorganisms.full.txt
-phenotype-relations pubmed,microbes-2019/phenotype-relations.full.txt
-phenotype-relations pubmed,microbes-2019/phenotype-relations.txt
-phenotypes pubmed,microbes-2019/phenotypes.full.txt
-relations pubmed,microbes-2019/relations.full.txt
-uses pubmed,microbes-2019/uses.full.txt
-uses-relations pubmed,microbes-2019/uses-relations.full.txt
--
GitLab
From 3645e05fe6727c0a0f73521f3997c6e22e44283a Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 14:54:15 +0000
Subject: [PATCH 03/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 40c76264..24294c6c 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -36,12 +36,14 @@ rule stats_cirm_BIA:
df2.to_csv(output.stats, index=False)
'''
-cirm | nb entites | count_lines(corpora/cirm/mapped_taxids.txt)
+cirm | nb entites | count_lines(corpora/cirm/mapped_bia_taxa.txt)
cirm | nb yeast entities | count_lines(corpora/cirm/mapped_yeast_taxa.txt)
-cirm | nb entites | count_lines(corpora/cirm/mapped_habitats.txt)
+cirm | nb entites | count_lines(corpora/cirm/mapped_bia_habitats.txt)
cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_yeast_habitats.txt)
+cirm | nb entites | count_lines(corpora/cirm/mapped_cfbp_habitats.txt)
+cirm | nb yeast habitats | count_lines(corpora/cirm/mapped_cfbp_habitats.txt)
'''
-SORTIES_CIRM= ["mapped_taxids.txt", "mapped_yeast_taxa.txt", "mapped_habitats.txt", "mapped_yeast_habitats.txt" ]
+SORTIES_CIRM= ["mapped_bia_taxa.txt", "mapped_yeast_taxa.txt", "mapped_cfbp_taxa.txt", "mapped_bia_habitats.txt", "mapped_yeast_habitats.txt", "mapped_cfbp_habitats.txt" ]
'''
'''
rule stats_cirm_Levure:
@@ -126,7 +128,7 @@ dsmz | nb entites | count_lines(corpora/dsmz/mapped_taxids.txt)
dsmz | nb habitats | count_lines(corpora/dsmz/mapped_habitats.txt)
'''
ENTREES_DSMZ = ["dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv" ]
-SORTIES_DSMZ = ["mapped_taxids.txt", "mapped_habitats.txt" ]
+SORTIES_DSMZ = [ "mapped_habitats.txt" ]
FILES_DSMZ = ENTREES_DSMZ + SORTIES_DSMZ
'''
'''
--
GitLab
From 9a40bd17ecfce91cf670940b114a30214c04973b Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:08:43 +0000
Subject: [PATCH 04/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 24294c6c..df88e56f 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -181,6 +181,17 @@ SORTIES_PUBMED = ["relations.full.txt", "phenotype-relations.full.txt", "uses-re
FILES_PUBMED = ENTREES_PUBMED + SORTIES_PUBMED
+'''
+'''
+rule get_list_of_batches:
+ input:
+ batches="corpora/pubmed/batches/"
+ output
+ list="corpora/pubmed/list_of_batches.txt"
+ shell:"""
+ ls {input.batches}/*/batch.xml >> {ouput.list}
+ """
+
'''
'''
--
GitLab
From 70bfe1435116df2ac3720045cc8f0e974e41b369 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:09:37 +0000
Subject: [PATCH 05/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index df88e56f..aa17d806 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -186,7 +186,7 @@ FILES_PUBMED = ENTREES_PUBMED + SORTIES_PUBMED
rule get_list_of_batches:
input:
batches="corpora/pubmed/batches/"
- output
+ output:
list="corpora/pubmed/list_of_batches.txt"
shell:"""
ls {input.batches}/*/batch.xml >> {ouput.list}
--
GitLab
From 278db9a0727524647edb5249b90cd698d7f9ee61 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:10:27 +0000
Subject: [PATCH 06/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index aa17d806..83b7c314 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -189,7 +189,7 @@ rule get_list_of_batches:
output:
list="corpora/pubmed/list_of_batches.txt"
shell:"""
- ls {input.batches}/*/batch.xml >> {ouput.list}
+ ls {input.batches}/*/batch.xml >> {output.list}
"""
'''
--
GitLab
From 214621797783d00da11a67553ce8300e6288e0f2 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:20:48 +0000
Subject: [PATCH 07/21] Update corpora/florilege/dates.metadata
---
corpora/florilege/dates.metadata | 7 +++++++
1 file changed, 7 insertions(+)
create mode 100644 corpora/florilege/dates.metadata
diff --git a/corpora/florilege/dates.metadata b/corpora/florilege/dates.metadata
new file mode 100644
index 00000000..b4b423ae
--- /dev/null
+++ b/corpora/florilege/dates.metadata
@@ -0,0 +1,7 @@
+
+cirm
+genbank
+dsmz
+pubmed
+ontobitope
+ncbi taxo
--
GitLab
From 4989fb62d9fa913916936d489165ca9e1cf130b7 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:32:18 +0000
Subject: [PATCH 08/21] Update corpora/florilege/dates.metadata,
corpora/florilege/labels.stats files
---
corpora/florilege/dates.metadata | 14 ++++++++------
corpora/florilege/labels.stats | 1 +
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/corpora/florilege/dates.metadata b/corpora/florilege/dates.metadata
index b4b423ae..85a7d9b9 100644
--- a/corpora/florilege/dates.metadata
+++ b/corpora/florilege/dates.metadata
@@ -1,7 +1,9 @@
-cirm
-genbank
-dsmz
-pubmed
-ontobitope
-ncbi taxo
+source,uri,valeur
+cirm,/db/maj/genbank/date,17-02-2021
+genbank,/db/maj/genbank/date,27-01-2021
+dsmz,/db/maj/dsmz/date,26-01-2018
+pubmed,/db/maj/pubmed/date,01-09-2021
+ontobitope,/db/maj/ontobitope/date,
+eval,migale/evaluation/BB19/date,14-04-2021
+ncbi,migale/ncbi/taxo/date,
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 9082013d..ef9a206d 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -40,3 +40,4 @@ eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,Bio
eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/pubmed/date
+ncbi_000,date de mise à jour de la taxo ncbi,migale/ncbi/taxo/date
--
GitLab
From f982664bce1a77b8eb9971408560f391a59007fa Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:35:11 +0000
Subject: [PATCH 09/21] Update corpora/florilege/dates.metadata,
corpora/florilege/labels.stats files
---
corpora/florilege/dates.metadata | 4 ++--
corpora/florilege/labels.stats | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/corpora/florilege/dates.metadata b/corpora/florilege/dates.metadata
index 85a7d9b9..3f1f97fc 100644
--- a/corpora/florilege/dates.metadata
+++ b/corpora/florilege/dates.metadata
@@ -4,6 +4,6 @@ cirm,/db/maj/genbank/date,17-02-2021
genbank,/db/maj/genbank/date,27-01-2021
dsmz,/db/maj/dsmz/date,26-01-2018
pubmed,/db/maj/pubmed/date,01-09-2021
-ontobitope,/db/maj/ontobitope/date,
+ontobitope,/db/maj/ontobitope/date,09-04-2021
eval,migale/evaluation/BB19/date,14-04-2021
-ncbi,migale/ncbi/taxo/date,
+ncbi,migale/ncbi/taxo/date,9-04-2021
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index ef9a206d..387bffaa 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -39,5 +39,5 @@ eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,Bio
eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
-ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/pubmed/date
+ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/ontobiotope/date
ncbi_000,date de mise à jour de la taxo ncbi,migale/ncbi/taxo/date
--
GitLab
From 0d53e1716f36efc30d8e4844a1180d60b0b0e36c Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:40:22 +0000
Subject: [PATCH 10/21] Update generate_stats.snakefile,
corpora/florilege/dates.meta files
---
corpora/florilege/{dates.metadata => dates.meta} | 0
generate_stats.snakefile | 6 ++++--
2 files changed, 4 insertions(+), 2 deletions(-)
rename corpora/florilege/{dates.metadata => dates.meta} (100%)
diff --git a/corpora/florilege/dates.metadata b/corpora/florilege/dates.meta
similarity index 100%
rename from corpora/florilege/dates.metadata
rename to corpora/florilege/dates.meta
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 83b7c314..5b90183b 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -357,7 +357,6 @@ rule merge_all:
result.to_csv(output.result, index=False)
-
'''
merge
'''
@@ -365,11 +364,14 @@ rule joint_stats:
input:
full_r="corpora/florilege/stats.full.csv",
concepts="corpora/florilege/labels.stats"
+ dates="corpora/florilege/dates.meta"
output:
result="corpora/florilege/full_stats_with_labels.csv"
run:
import pandas
df1=pandas.read_csv(input.concepts)
df2=pandas.read_csv(input.full_r)
- df = pandas.merge(df1, df2, on="uri", how="left")
+ df3=pandas.read_csv(input.dates)
+ frames = [df1, df_2]
+ df = pandas.merge(df1, pandas.concat(frames), on="uri", how="left")
df.to_csv(output.result, index=False)
--
GitLab
From c14b509dec10f585268f6ac197f271f52b025773 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:41:38 +0000
Subject: [PATCH 11/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 5b90183b..822200f3 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -363,7 +363,7 @@ merge
rule joint_stats:
input:
full_r="corpora/florilege/stats.full.csv",
- concepts="corpora/florilege/labels.stats"
+ concepts="corpora/florilege/labels.stats",
dates="corpora/florilege/dates.meta"
output:
result="corpora/florilege/full_stats_with_labels.csv"
--
GitLab
From 42920f323cbfcec40f73fb57800bece774bca4ef Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:45:22 +0000
Subject: [PATCH 12/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 822200f3..8b19a7c5 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -369,9 +369,7 @@ rule joint_stats:
result="corpora/florilege/full_stats_with_labels.csv"
run:
import pandas
- df1=pandas.read_csv(input.concepts)
- df2=pandas.read_csv(input.full_r)
- df3=pandas.read_csv(input.dates)
- frames = [df1, df_2]
+ frames = [pandas.read_csv(input.concepts), pandas.read_csv(input.dates)]
+ df1=pandas.read_csv(input.full_r)
df = pandas.merge(df1, pandas.concat(frames), on="uri", how="left")
df.to_csv(output.result, index=False)
--
GitLab
From 4133de90de3d2e2efb617449f84cb5f6efcede59 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:49:38 +0000
Subject: [PATCH 13/21] Update generate_stats.snakefile
---
generate_stats.snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index 8b19a7c5..a7c6783f 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -369,7 +369,7 @@ rule joint_stats:
result="corpora/florilege/full_stats_with_labels.csv"
run:
import pandas
- frames = [pandas.read_csv(input.concepts), pandas.read_csv(input.dates)]
- df1=pandas.read_csv(input.full_r)
+ frames = [pandas.read_csv(input.full_r), pandas.read_csv(input.dates)]
+ df1=pandas.read_csv(input.concepts)
df = pandas.merge(df1, pandas.concat(frames), on="uri", how="left")
df.to_csv(output.result, index=False)
--
GitLab
From 19c021255816627cb3020b4041aa4c40880a369c Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 15:56:56 +0000
Subject: [PATCH 14/21] Update corpora/florilege/labels.stats,
corpora/florilege/dates.meta files
---
corpora/florilege/dates.meta | 2 +-
corpora/florilege/labels.stats | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/corpora/florilege/dates.meta b/corpora/florilege/dates.meta
index 3f1f97fc..fd191100 100644
--- a/corpora/florilege/dates.meta
+++ b/corpora/florilege/dates.meta
@@ -6,4 +6,4 @@ dsmz,/db/maj/dsmz/date,26-01-2018
pubmed,/db/maj/pubmed/date,01-09-2021
ontobitope,/db/maj/ontobitope/date,09-04-2021
eval,migale/evaluation/BB19/date,14-04-2021
-ncbi,migale/ncbi/taxo/date,9-04-2021
+ncbi,migale/maj/ncbi/taxo/date,9-04-2021
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 387bffaa..2e1ef135 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1,5 +1,5 @@
id,libelle,uri
-cirm_000, date de mise à jour des données cirm, /db/maj/genbank/date
+cirm_000,date de mise à jour des données cirm, /db/maj/genbank/date
cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
cirm_002,nombre d'entrées de cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_bia_taxa.txt
@@ -9,7 +9,7 @@ cirm_006,nombre d'habitats de cirm-Levure,cirm/mapped_yeast_habitats.txt
cirm_007,nombre d'entrées de cirm-cfpb,corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
cirm_006,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
cirm_006,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
-genbank_000, date de mise à jour des données genbank,/db/maj/genbank/date
+genbank_000,date de mise à jour des données genbank,/db/maj/genbank/date
genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
genbank_002,nombre de taxons de genbank,genbank/mapped_taxa.txt
genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
@@ -39,5 +39,5 @@ eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,Bio
eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
-ontobiotope_000, date de mise à jour de ontobiotope,/db/maj/ontobiotope/date
-ncbi_000,date de mise à jour de la taxo ncbi,migale/ncbi/taxo/date
+ontobiotope_000,date de mise à jour de ontobiotope,/db/maj/ontobiotope/date
+ncbi_000,date de mise à jour de la taxo ncbi,migale/maj/ncbi/taxo/date
--
GitLab
From 37c530d2e9636b874e7b73a3c9747eef0afb4836 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 16:08:47 +0000
Subject: [PATCH 15/21] Update corpora/florilege/labels.stats,
generate_stats.snakefile files
---
corpora/florilege/labels.stats | 10 +++++-----
generate_stats.snakefile | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 2e1ef135..daadec61 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -4,26 +4,26 @@ cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_0
cirm_002,nombre d'entrées de cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_bia_taxa.txt
cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
-cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_habitats.txt
+cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_bia_habitats.txt
cirm_006,nombre d'habitats de cirm-Levure,cirm/mapped_yeast_habitats.txt
cirm_007,nombre d'entrées de cirm-cfpb,corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
cirm_006,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
cirm_006,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
genbank_000,date de mise à jour des données genbank,/db/maj/genbank/date
genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
-genbank_002,nombre de taxons de genbank,genbank/mapped_taxa.txt
+genbank_002,nombre de taxons de genbank,genbank/mapped_taxids.txt
genbank_003,nombre d'entités du type #Habitat de genbank,genbank/mapped_habitats.txt
dsmz_000, date de mise à jour des données de dsmz,/db/maj/dsmz/date
dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-key=taxid.tsv
-dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxa.txt
+dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
pubmed_004,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
-pubmed_005,nombre de relations de type #Use pubmed,microbes-2019/uses.full.txt
-pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/habitat-relations.full.txt
+pubmed_005,nombre d'entités du type #Use de pubmed,microbes-2019/uses.full.txt
+pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
pubmed_007,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
pubmed_008,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
diff --git a/generate_stats.snakefile b/generate_stats.snakefile
index a7c6783f..4e1d2eb3 100644
--- a/generate_stats.snakefile
+++ b/generate_stats.snakefile
@@ -16,7 +16,7 @@ SOURCES=["cirm", "genbank", "dsmz", "pubmed", "BioNLP-OST-2019"]
cirm | nb entrees | count_lines(corpora/cirm/BIA_2021/florilege_export_final_17_02_21.xlsx)
cirm | nb yeast entrees | count_lines(corpora/cirm/Levures_2021/Florilege_21012021.xlsx)
'''
-ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx"]
+ENTREES_CIRM = ["BIA_2021/florilege_export_final_17_02_21.xlsx", "Levures_2021/Florilege_21012021.xlsx", "CFBP_2020/CFPB_22_sept_2020_Type.xlsx"]
rule stats_cirm_BIA:
input:
file="corpora/cirm/{file}"
--
GitLab
From 5eba87bc503fa9608994f1136473bb7211115da8 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 16:18:57 +0000
Subject: [PATCH 16/21] Update corpora/florilege/labels.stats
---
corpora/florilege/labels.stats | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index daadec61..c50abc0a 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -1,5 +1,5 @@
id,libelle,uri
-cirm_000,date de mise à jour des données cirm, /db/maj/genbank/date
+cirm_000,date de mise à jour des données cirm,/db/maj/genbank/date
cirm_001,nombre d'entrées de cirm-BIA,cirm/BIA_2021/florilege_export_final_17_02_21.xlsx
cirm_002,nombre d'entrées de cirm-Levure,cirm/Levures_2021/Florilege_21012021.xlsx
cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_bia_taxa.txt
@@ -26,18 +26,18 @@ pubmed_005,nombre d'entités du type #Use de pubmed,microbes-2019/uses.full.txt
pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
pubmed_007,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
pubmed_008,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
-eval_001, corpus utilisés, https://sites.google.com/view/bb-2019
-eval_002, date d'évaluation, migale/evaluation/BB19/date
-eval_BB19-norm+ner_001, mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
-eval_BB19-norm+ner_002, score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
-eval_BB19-norm+ner_002, score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
-eval_BB19-norm+ner_003, score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
-eval_BB19-norm+ner_004, score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
-eval_BB19-rel+ner_001, mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
-eval_BB19-rel+ner_002, score global sur la prédiction de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Standard_scoring
-eval_BB19-rel+ner_002, score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
-eval_BB19-rel+ner_003, score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
-eval_BB19-kb+ner_001, mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
-eval_BB19-kb+ner_002, score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
+eval_001,corpus utilisés,https://sites.google.com/view/bb-2019
+eval_002,date d'évaluation,migale/evaluation/BB19/date
+eval_BB19-norm+ner_001,mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
+eval_BB19-norm+ner_002,score global sur la prédiction de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Standard_scoring
+eval_BB19-norm+ner_002,score sur la prédiction des taxons de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Microorganism
+eval_BB19-norm+ner_003,score sur la prédiction des phénotypes de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Phenotype
+eval_BB19-norm+ner_004,score sur la prédiction des habitats de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Habitat
+eval_BB19-rel+ner_001,mesure pour l'evaluation de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Mesure
+eval_BB19-rel+ner_002,score global sur la prédiction de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Standard_scoring
+eval_BB19-rel+ner_002,score sur la prédiction des Lives-In de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Lives_In
+eval_BB19-rel+ner_003,score sur la prédiction des Exhibits de BB19-rel+ner,BioNLP-OST-2019/BB19-rel+ner#Exhibits
+eval_BB19-kb+ner_001,mesure pour l'evaluation de BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Mesure
+eval_BB19-kb+ner_002,score moyen sur BB19-kb+ner,BioNLP-OST-2019/BB19-kb+ner#Standard_scoring
ontobiotope_000,date de mise à jour de ontobiotope,/db/maj/ontobiotope/date
ncbi_000,date de mise à jour de la taxo ncbi,migale/maj/ncbi/taxo/date
--
GitLab
From 79f33d0b1a4932966f19da4c70e59e2b71fdb78d Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 16:22:44 +0000
Subject: [PATCH 17/21] Update corpora/florilege/labels.stats
---
corpora/florilege/labels.stats | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index c50abc0a..1a2b5711 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -18,14 +18,14 @@ dsmz_001,nombre d'entrées de dsmz,dsmz/dsmz-data/category=from_ncbi_taxonomy-ke
dsmz_002,nombre de taxon venant de dsmz,dsmz/mapped_taxids.txt
dsmz_003,nombre d'entités de type #Habitat de dsmz,dsmz/mapped_habitats.txt
pubmed_000, date de mise à jour du corpus pubmed,/db/maj/pubmed/date
-pubmed_001,nombre de batches (x1000) pubmed,microbes-2019/list_of_batches.txt
-pubmed_002,nombre d'entités du type #Habitat de pubmed,microbes-2019/habitats.full.txt
-pubmed_003,nombre d'entités du type #Taxon pubmed,microbes-2019/microorganisms.full.txt
-pubmed_004,nombre d'entités du type #Phenotype de pubmed,microbes-2019/phenotypes.full.txt
-pubmed_005,nombre d'entités du type #Use de pubmed,microbes-2019/uses.full.txt
-pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,microbes-2019/relations.full.txt
-pubmed_007,nombre de relations du type #Phenotype-Taxon pubmed,microbes-2019/phenotype-relations.full.txt
-pubmed_008,nombre de relations du type #Use-Taxon pubmed,microbes-2019/uses-relations.full.txt
+pubmed_001,nombre de batches (x1000) pubmed,pubmed/list_of_batches.txt
+pubmed_002,nombre d'entités du type #Habitat de pubmed,pubmed/habitats.full.txt
+pubmed_003,nombre d'entités du type #Taxon pubmed,pubmed/microorganisms.full.txt
+pubmed_004,nombre d'entités du type #Phenotype de pubmed,pubmed/phenotypes.full.txt
+pubmed_005,nombre d'entités du type #Use de pubmed,pubmed/uses.full.txt
+pubmed_006,nombre de relations du type #Taxon-Habitat de pubmed,pubmed/relations.full.txt
+pubmed_007,nombre de relations du type #Phenotype-Taxon pubmed,pubmed/phenotype-relations.full.txt
+pubmed_008,nombre de relations du type #Use-Taxon pubmed,pubmed/uses-relations.full.txt
eval_001,corpus utilisés,https://sites.google.com/view/bb-2019
eval_002,date d'évaluation,migale/evaluation/BB19/date
eval_BB19-norm+ner_001,mesure pour l'evaluation de BB19-norm+ner,BioNLP-OST-2019/BB19-norm+ner#Mesure
--
GitLab
From f72e4188efd9145c847e945b76e7d6e33743d35d Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 16:23:48 +0000
Subject: [PATCH 18/21] Update corpora/florilege/dates.meta
---
corpora/florilege/dates.meta | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/corpora/florilege/dates.meta b/corpora/florilege/dates.meta
index fd191100..d0b166ff 100644
--- a/corpora/florilege/dates.meta
+++ b/corpora/florilege/dates.meta
@@ -4,6 +4,6 @@ cirm,/db/maj/genbank/date,17-02-2021
genbank,/db/maj/genbank/date,27-01-2021
dsmz,/db/maj/dsmz/date,26-01-2018
pubmed,/db/maj/pubmed/date,01-09-2021
-ontobitope,/db/maj/ontobitope/date,09-04-2021
+ontobitope,/db/maj/ontobiotope/date,09-04-2021
eval,migale/evaluation/BB19/date,14-04-2021
ncbi,migale/maj/ncbi/taxo/date,9-04-2021
--
GitLab
From c72aab946cc18fea201af71f226686176483c6d2 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 17:26:16 +0000
Subject: [PATCH 19/21] Update corpora/florilege/labels.stats,
corpora/florilege/dates.meta files
---
corpora/florilege/dates.meta | 1 +
corpora/florilege/labels.stats | 4 ++--
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/corpora/florilege/dates.meta b/corpora/florilege/dates.meta
index d0b166ff..4f73dce5 100644
--- a/corpora/florilege/dates.meta
+++ b/corpora/florilege/dates.meta
@@ -6,4 +6,5 @@ dsmz,/db/maj/dsmz/date,26-01-2018
pubmed,/db/maj/pubmed/date,01-09-2021
ontobitope,/db/maj/ontobiotope/date,09-04-2021
eval,migale/evaluation/BB19/date,14-04-2021
+eval,corpus d'evaluation,https://sites.google.com/view/bb-2019,Bacteria Bitope 2019
ncbi,migale/maj/ncbi/taxo/date,9-04-2021
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 1a2b5711..47867232 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -7,8 +7,8 @@ cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_bia_habitats.txt
cirm_006,nombre d'habitats de cirm-Levure,cirm/mapped_yeast_habitats.txt
cirm_007,nombre d'entrées de cirm-cfpb,corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
-cirm_006,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
-cirm_006,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
+cirm_008,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
+cirm_009,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
genbank_000,date de mise à jour des données genbank,/db/maj/genbank/date
genbank_001,nombre d'entrées de genbank,genbank/GenBank_extraction_20210127.tsv
genbank_002,nombre de taxons de genbank,genbank/mapped_taxids.txt
--
GitLab
From a8e84aa3db9fe198388e7451d78cf88fa9b07a5d Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 17:35:39 +0000
Subject: [PATCH 20/21] Update corpora/florilege/dates.meta
---
corpora/florilege/dates.meta | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/corpora/florilege/dates.meta b/corpora/florilege/dates.meta
index 4f73dce5..42ca6be6 100644
--- a/corpora/florilege/dates.meta
+++ b/corpora/florilege/dates.meta
@@ -6,5 +6,5 @@ dsmz,/db/maj/dsmz/date,26-01-2018
pubmed,/db/maj/pubmed/date,01-09-2021
ontobitope,/db/maj/ontobiotope/date,09-04-2021
eval,migale/evaluation/BB19/date,14-04-2021
-eval,corpus d'evaluation,https://sites.google.com/view/bb-2019,Bacteria Bitope 2019
+eval,https://sites.google.com/view/bb-2019,Bacteria Bitope 2019
ncbi,migale/maj/ncbi/taxo/date,9-04-2021
--
GitLab
From 86133f30260931b22b6cec211a3cc668df5fca69 Mon Sep 17 00:00:00 2001
From: Mouhamadou Ba <mandiayba@gmail.com>
Date: Wed, 14 Apr 2021 17:39:42 +0000
Subject: [PATCH 21/21] Update corpora/florilege/labels.stats
---
corpora/florilege/labels.stats | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/corpora/florilege/labels.stats b/corpora/florilege/labels.stats
index 47867232..12383268 100644
--- a/corpora/florilege/labels.stats
+++ b/corpora/florilege/labels.stats
@@ -6,7 +6,7 @@ cirm_003,nombre de taxons de cirm-BIA,cirm/mapped_bia_taxa.txt
cirm_004,nombre de taxons de cirm-Levure,cirm/mapped_yeast_taxa.txt
cirm_005,nombre d'habitats de cirm-BIA,cirm/mapped_bia_habitats.txt
cirm_006,nombre d'habitats de cirm-Levure,cirm/mapped_yeast_habitats.txt
-cirm_007,nombre d'entrées de cirm-cfpb,corpora/cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
+cirm_007,nombre d'entrées de cirm-cfpb,cirm/CFBP_2020/CFPB_22_sept_2020_Type.xlsx
cirm_008,nombre de taxons de cirm-cfpb,cirm/mapped_cfbp_taxa.txt
cirm_009,nombre d'habitats de cirm-cfpb,cirm/mapped_cfbp_habitats.txt
genbank_000,date de mise à jour des données genbank,/db/maj/genbank/date
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