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authorLLTommy2020-06-08 19:18:06 +0200
committerGitHub2020-06-08 19:18:06 +0200
commit39eca644ed4a0a86510ae0b8afb8da9207d9750a (patch)
tree8c4b23c7c016275a57a96a018ea271f6c067824b /scripts/dict_ontology_standardization
parent80cfaba31a99d0c34722312c1b1a69a139477510 (diff)
parente1447dedb1a2a1a03957e56c812acdedf47d43fb (diff)
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Merge pull request #74 from AndreaGuarracino/patch-16
from_genbank_to_fasta_and_yaml script update
Diffstat (limited to 'scripts/dict_ontology_standardization')
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv13
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv2
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv7
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