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| author | LLTommy | 2020-06-08 19:18:06 +0200 |
|---|---|---|
| committer | GitHub | 2020-06-08 19:18:06 +0200 |
| commit | 39eca644ed4a0a86510ae0b8afb8da9207d9750a (patch) | |
| tree | 8c4b23c7c016275a57a96a018ea271f6c067824b /scripts/dict_ontology_standardization | |
| parent | 80cfaba31a99d0c34722312c1b1a69a139477510 (diff) | |
| parent | e1447dedb1a2a1a03957e56c812acdedf47d43fb (diff) | |
| download | bh20-seq-resource-39eca644ed4a0a86510ae0b8afb8da9207d9750a.tar.gz bh20-seq-resource-39eca644ed4a0a86510ae0b8afb8da9207d9750a.tar.lz bh20-seq-resource-39eca644ed4a0a86510ae0b8afb8da9207d9750a.zip | |
Merge pull request #74 from AndreaGuarracino/patch-16
from_genbank_to_fasta_and_yaml script update
Diffstat (limited to 'scripts/dict_ontology_standardization')
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 |