Resolve "Utilisation du fichier de config"

Closes #59 (closed)

config/config.yaml

 # params value
 
-ONTOBIOTOPE: "ancillaries/BioNLP-OST+EnovFood.obo"
-
-USE: "ancillaries/BioNLP-OST+EnovFood-Use.obo"
-
-ONTONAMES: "BioNLP-OST+EnovFood-Habitat BioNLP-OST+EnovFood-Phenotype BioNLP-OST+EnovFood-Use"
-
-NCBI_TAXO_ID: "ancillaries/supertaxo/taxa+id_full.txt"
 
-NCBI_TAXO_MICROORGANISMS: "ancillaries/supertaxo/taxid_microorganisms.txt"
-
-NCBI_TAXO_NAMES: "ancillaries/supertaxo/names.dmp"
-
-MAP_BACDIVE_TAXID: "ancillaries/supertaxo/dsmz-match/bacdive-to-taxid.txt"
+# ontobiotope
+ONTOBIOTOPE: "ancillaries/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"
+
+# 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"
 
 ## cirm
 CIRM_FOLDER_NAME : "cirm"
 CIRM_CORPUS_HOME : "corpora/cirm/"
-CIRM_CORPUS : "corpora/cirm/2019-07-05/extraction_3-fv.csv"
+# bia
+CIRM_BIA_CORPUS : "corpora/cirm/BIA_2022/Omnicrobe_03-2022.xlsx"
+		#taxa_index='2', change these values into the cirm snakefile
+		#strain_index='1',
+		#habitat_index='15'
+# yeast
+CIRM_YEAST_CORPUS : "corpora/cirm/Levures_2021/Florilege_23082021.xlsx"
+		#taxa_index='1', change these values into the cirm snakefile
+		#habitat_index='10,11'
+# cfbp
+CIRM_CFBP_CORPUS : "corpora/cirm/CFBP_2022/ExportBaseCIRM-CFBP_Omnicrobe_8mars2022.xlsx"
+		#taxa_index='17', change these values into the cirm snakefile
+		#strain_index='0',
+		#habitat_index='27,3,31,29,26'
+        
 CIRM_TAXA_CORPUS : ""
 CIRM_HABITAT_CORPUS : ""
 CIRM_RESULT : "corpora/cirm/test.txt"
@@ -29,6 +46,7 @@ GENBANK_CORPUS : "corpora/genbank/req1_sup800_bacteria-descriptors.csv"
 GENBANK_TAXA_CORPUS : ""
 GENBANK_HABITAT_CORPUS : ""
 GENBANK_RESULT : "corpora/genbank/test-3.2.txt"
+GENBANK_DB : "/db/genbank/current/flat"
 
 
 ## dsmz
@@ -47,6 +65,7 @@ PUBMED_HABITAT_RESULT : "ancillaries/Florilege/2019-12-12/PubMed-Habitat-2019-12
 PUBMED_PHENOTYPE_RESULT : "ancillaries/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"
 
 ## bionlp-ost
 BIONLPOST_BATCHES_HOME : "corpora/BioNLP-OST-2019/batches"