diff options
Diffstat (limited to 'scripts')
4 files changed, 34 insertions, 8 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 7e83564..85d4e8a 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -12,6 +12,9 @@ Armenia,http://www.wikidata.org/entity/Q399 Australia,http://www.wikidata.org/entity/Q408 Australia: Queensland,http://www.wikidata.org/entity/Q36074 Australia: Victoria,http://www.wikidata.org/entity/Q36687 +"Australia: Melbourne, Victoria",http://www.wikidata.org/entity/Q3141 +Australia: Northern Territory,http://www.wikidata.org/entity/Q3235 +Australia: NSW,http://www.wikidata.org/entity/Q3224 Austria,http://www.wikidata.org/entity/Q40 Azerbaijan,http://www.wikidata.org/entity/Q227 Bahrain,http://www.wikidata.org/entity/Q398 @@ -31,8 +34,10 @@ Bulgaria,http://www.wikidata.org/entity/Q219 Burkina Faso,http://www.wikidata.org/entity/Q965 Burundi,http://www.wikidata.org/entity/Q967 Cambodia,http://www.wikidata.org/entity/Q424 +Cambodia:Sihanoukville,http://www.wikidata.org/entity/Q18207676 Cameroon,http://www.wikidata.org/entity/Q1009 Canada,http://www.wikidata.org/entity/Q16 +Canada: Toronto,http://www.wikidata.org/entity/Q172 Cape Verde,http://www.wikidata.org/entity/Q1011 Central African Republic,http://www.wikidata.org/entity/Q929 Chad,http://www.wikidata.org/entity/Q657 @@ -65,12 +70,13 @@ China: Jiangxi,http://www.wikidata.org/entity/Q57052 China: Jilin,http://www.wikidata.org/entity/Q45208 China: Liaoning,http://www.wikidata.org/entity/Q43934 China: Macau,http://www.wikidata.org/entity/Q14773 -China: Nanchang,https://www.wikidata.org/wiki/Q171943 +China: Nanchang,http://www.wikidata.org/entity/Q171943 China: Ningxia Hui Autonomous Region,http://www.wikidata.org/entity/Q57448 China: Qinghai,http://www.wikidata.org/entity/Q45833 China: Shaanxi,http://www.wikidata.org/entity/Q47974 China: Shandong,http://www.wikidata.org/entity/Q43407 China: Shanghai,http://www.wikidata.org/entity/Q8686 +China:Shanghai,http://www.wikidata.org/entity/Q8686 China: Shanxi,http://www.wikidata.org/entity/Q46913 China: Shenzhen,http://www.wikidata.org/entity/Q15174 China: Sichuan,http://www.wikidata.org/entity/Q19770 @@ -111,11 +117,13 @@ 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 +Germany: Bavaria,http://www.wikidata.org/entity/Q980 +Germany: Dusseldorf,http://www.wikidata.org/entity/Q1718 +Germany: Heinsberg,http://www.wikidata.org/entity/Q14833 +Germany: Starnberg,http://www.wikidata.org/entity/Q61936 Ghana,http://www.wikidata.org/entity/Q117 Greece,http://www.wikidata.org/entity/Q41 -Greece: Athens,https://www.wikidata.org/wiki/Q1524 +Greece: Athens,http://www.wikidata.org/entity/Q1524 Grenada,http://www.wikidata.org/entity/Q769 Guatemala,http://www.wikidata.org/entity/Q774 Guinea,http://www.wikidata.org/entity/Q1006 @@ -139,8 +147,8 @@ 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: Lazio,http://www.wikidata.org/entity/Q1282 +Italy: Palermo,http://www.wikidata.org/entity/Q2656 Italy: Rome,http://www.wikidata.org/entity/Q220 Ivory Coast,http://www.wikidata.org/entity/Q1008 Jamaica,http://www.wikidata.org/entity/Q766 @@ -181,7 +189,7 @@ Mozambique,http://www.wikidata.org/entity/Q1029 Myanmar,http://www.wikidata.org/entity/Q836 Namibia,http://www.wikidata.org/entity/Q1030 Nauru,http://www.wikidata.org/entity/Q697 -Netherlands: Milheeze,https://www.wikidata.org/wiki/Q3314115 +Netherlands: Milheeze,http://www.wikidata.org/entity/Q3314115 Nepal,http://www.wikidata.org/entity/Q837 New Zealand,http://www.wikidata.org/entity/Q664 Nicaragua,http://www.wikidata.org/entity/Q811 @@ -269,10 +277,14 @@ USA: AK,http://www.wikidata.org/entity/Q797 USA: AL,http://www.wikidata.org/entity/Q173 USA: AR,http://www.wikidata.org/entity/Q1612 USA: AZ,http://www.wikidata.org/entity/Q816 +USA: Arizona,http://www.wikidata.org/entity/Q816 USA: CA,http://www.wikidata.org/entity/Q99 +USA: California,http://www.wikidata.org/entity/Q99 +USA:California,http://www.wikidata.org/entity/Q99 "USA: CA, San Diego County",http://www.wikidata.org/entity/Q108143 USA: CO,http://www.wikidata.org/entity/Q1261 USA: CT,http://www.wikidata.org/entity/Q779 +USA: Connecticut,http://www.wikidata.org/entity/Q779 USA: DC,http://www.wikidata.org/entity/Q3551781 USA: DE,http://www.wikidata.org/entity/Q1393 USA: FL,http://www.wikidata.org/entity/Q812 @@ -287,7 +299,7 @@ USA: IN,http://www.wikidata.org/entity/Q1415 USA: KS,http://www.wikidata.org/entity/Q1558 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: New Orleans, LA",http://www.wikidata.org/entity/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 @@ -295,6 +307,8 @@ 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:Minnesota,http://www.wikidata.org/entity/Q1527 +USA: Minnesota,http://www.wikidata.org/entity/Q1527 USA: MO,http://www.wikidata.org/entity/Q1581 USA: MS,http://www.wikidata.org/entity/Q1494 USA: MT,http://www.wikidata.org/entity/Q1212 @@ -323,8 +337,10 @@ 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:Virginia,http://www.wikidata.org/entity/Q1370 USA: VT,http://www.wikidata.org/entity/Q16551 USA: WA,http://www.wikidata.org/entity/Q1223 +USA: Washington,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 diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index 0d2120c..102d458 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -1,4 +1,6 @@ Homo sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 +human,http://purl.obolibrary.org/obo/NCBITaxon_9606 +Human,http://purl.obolibrary.org/obo/NCBITaxon_9606 Mustela lutreola,http://purl.obolibrary.org/obo/NCBITaxon_9666 Manis javanica,http://purl.obolibrary.org/obo/NCBITaxon_9974 Felis catus,http://purl.obolibrary.org/obo/NCBITaxon_9685 diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv index 49cb6b7..110e90b 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -1,6 +1,13 @@ 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 +NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173 +Illumian NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566 +Illumina NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566 +NextSeq550,http://www.ebi.ac.uk/efo/EFO_0008566 +NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566 +Illumina MiniSeq,http://www.ebi.ac.uk/efo/EFO_0008636 +Illumina NovaSeq 6000,http://www.ebi.ac.uk/efo/EFO_0008637 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 diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv index 18b986c..0fa2219 100644 --- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv +++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv @@ -14,6 +14,7 @@ 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 +oralpharyngeal,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 |