Merge pull request #74 from AndreaGuarracino/patch-16

from_genbank_to_fasta_and_yaml script update

3 files changed, 21 insertions, 1 deletions

diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 6b43137..7e83564 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -111,9 +111,11 @@ France,http://www.wikidata.org/entity/Q142
 Gabon,http://www.wikidata.org/entity/Q1000
 Georgia,http://www.wikidata.org/entity/Q230
 Germany,http://www.wikidata.org/entity/Q183
+Germany: Bavaria,https://www.wikidata.org/wiki/Q980
 Germany: Dusseldorf,https://www.wikidata.org/wiki/Q1718
 Ghana,http://www.wikidata.org/entity/Q117
 Greece,http://www.wikidata.org/entity/Q41
+Greece: Athens,https://www.wikidata.org/wiki/Q1524
 Grenada,http://www.wikidata.org/entity/Q769
 Guatemala,http://www.wikidata.org/entity/Q774
 Guinea,http://www.wikidata.org/entity/Q1006
@@ -125,6 +127,7 @@ Hungary,http://www.wikidata.org/entity/Q28
 Iceland,http://www.wikidata.org/entity/Q189
 Icelandic Commonwealth,http://www.wikidata.org/entity/Q62389
 India,http://www.wikidata.org/entity/Q668
+India: Ahmedabad,http://www.wikidata.org/entity/Q1070
 India: Kerala State,http://www.wikidata.org/entity/Q1186
 India: Rajkot,http://www.wikidata.org/entity/Q1815245
 Indonesia,http://www.wikidata.org/entity/Q252
@@ -136,6 +139,8 @@ Ireland,http://www.wikidata.org/entity/Q27
 Israel,http://www.wikidata.org/entity/Q801
 Italy,http://www.wikidata.org/entity/Q38
 Italy: Cagliari,http://www.wikidata.org/entity/Q1897
+Italy: Lazio,https://www.wikidata.org/wiki/Q1282
+Italy: Palermo,https://www.wikidata.org/wiki/Q2656
 Italy: Rome,http://www.wikidata.org/entity/Q220
 Ivory Coast,http://www.wikidata.org/entity/Q1008
 Jamaica,http://www.wikidata.org/entity/Q766
@@ -272,6 +277,7 @@ USA: DC,http://www.wikidata.org/entity/Q3551781
 USA: DE,http://www.wikidata.org/entity/Q1393
 USA: FL,http://www.wikidata.org/entity/Q812
 USA: GA,http://www.wikidata.org/entity/Q1428
+USA: Georgia,http://www.wikidata.org/entity/Q1428
 USA: HI,http://www.wikidata.org/entity/Q782
 USA: IA,http://www.wikidata.org/entity/Q1546
 USA: ID,http://www.wikidata.org/entity/Q1221
@@ -283,9 +289,11 @@ USA: KY,http://www.wikidata.org/entity/Q1603
 USA: LA,http://www.wikidata.org/entity/Q1588
 "USA: New Orleans, LA",https://www.wikidata.org/wiki/Q34404
 USA: MA,http://www.wikidata.org/entity/Q771
+USA: Massachusetts,http://www.wikidata.org/entity/Q771
 USA: MD,http://www.wikidata.org/entity/Q1391
 USA: ME,http://www.wikidata.org/entity/Q724
 USA: MI,http://www.wikidata.org/entity/Q1166
+USA: Michigan,http://www.wikidata.org/entity/Q1166
 USA: MN,http://www.wikidata.org/entity/Q1527
 USA: MO,http://www.wikidata.org/entity/Q1581
 USA: MS,http://www.wikidata.org/entity/Q1494
@@ -301,6 +309,7 @@ USA: NV,http://www.wikidata.org/entity/Q1227
 USA: NY,http://www.wikidata.org/entity/Q1384
 USA: New York,http://www.wikidata.org/entity/Q1384
 USA: OH,http://www.wikidata.org/entity/Q1397
+USA: Ohio,http://www.wikidata.org/entity/Q1397
 USA: OK,http://www.wikidata.org/entity/Q1649
 USA: OR,http://www.wikidata.org/entity/Q824
 USA: PA,http://www.wikidata.org/entity/Q1400
@@ -313,9 +322,11 @@ USA: TN,http://www.wikidata.org/entity/Q1509
 USA: TX,http://www.wikidata.org/entity/Q1439
 USA: UT,http://www.wikidata.org/entity/Q829
 USA: VA,http://www.wikidata.org/entity/Q1370
+USA: Virginia,http://www.wikidata.org/entity/Q1370
 USA: VT,http://www.wikidata.org/entity/Q16551
 USA: WA,http://www.wikidata.org/entity/Q1223
 USA: WI,http://www.wikidata.org/entity/Q1537
+USA: Wisconsin,http://www.wikidata.org/entity/Q1537
 USA: WV,http://www.wikidata.org/entity/Q1371
 USA: WY,http://www.wikidata.org/entity/Q1214
 Uzbekistan,http://www.wikidata.org/entity/Q265
@@ -328,4 +339,4 @@ Viet Nam: Ho Chi Minh city,http://www.wikidata.org/entity/Q1854
 Vietnam,http://www.wikidata.org/entity/Q881
 Yemen,http://www.wikidata.org/entity/Q805
 Zambia,http://www.wikidata.org/entity/Q953
-Zimbabwe,http://www.wikidata.org/entity/Q954
\ No newline at end of file
+Zimbabwe,http://www.wikidata.org/entity/Q954
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
index 0c92c61..49cb6b7 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -1,8 +1,10 @@
 Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
 Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
+NextSeq500,http://www.ebi.ac.uk/efo/EFO_0009173
 Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818
+Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818
 Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632
 Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index 7fa67f8..18b986c 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -1,4 +1,5 @@
 nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal swabs,http://purl.obolibrary.org/obo/NCIT_C155831
 nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
 nasopharyngeal,http://purl.obolibrary.org/obo/NCIT_C155831
 respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831
@@ -12,10 +13,16 @@ nasopharyngeal (throat) washings,http://purl.obolibrary.org/obo/NCIT_C155831
 oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
 throat swab,http://purl.obolibrary.org/obo/NCIT_C155835
 oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
+Oropharyngal,http://purl.obolibrary.org/obo/NCIT_C155835
+Oral-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
+Oro-pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
+Oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
+oro pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
 buccal swab,http://purl.obolibrary.org/obo/NCIT_C155835
 throat washing,http://purl.obolibrary.org/obo/NCIT_C155835
 Throat Swab,http://purl.obolibrary.org/obo/NCIT_C155835
 throat (oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835
+Throat (Oropharyngeal) swab,http://purl.obolibrary.org/obo/NCIT_C155835
 bronchoalveolar lavage fluid,http://purl.obolibrary.org/obo/NCIT_C13195
 swab,http://purl.obolibrary.org/obo/NCIT_C13195
 oral swab,http://purl.obolibrary.org/obo/NCIT_C13195