diff options
Diffstat (limited to 'scripts/dict_ontology_standardization')
3 files changed, 59 insertions, 2 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 204f7f2..4bea3ec 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -284,6 +284,7 @@ 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: California, Monterey County",http://www.wikidata.org/entity/Q108072 USA: CO,http://www.wikidata.org/entity/Q1261 USA: CT,http://www.wikidata.org/entity/Q779 USA: Connecticut,http://www.wikidata.org/entity/Q779 @@ -301,8 +302,9 @@ 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:Los Angeles,http://www.wikidata.org/entity/Q65 -"USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404 +"USA: SLIDELL, LA, LA",https://www.wikidata.org/wiki/Q988156 +"USA: Slidell, LA, LA",https://www.wikidata.org/wiki/Q988156 +"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 @@ -336,6 +338,33 @@ USA: SC,http://www.wikidata.org/entity/Q1456 USA: South Carolina,http://www.wikidata.org/entity/Q1456 USA: SD,http://www.wikidata.org/entity/Q1211 "USA: Snohomish County, WA",http://www.wikidata.org/entity/Q110403 +"USA: Washington,Snohomish County",http://www.wikidata.org/entity/Q110403 +"USA: Washington, Snohomish County",http://www.wikidata.org/entity/Q110403 +"USA: Washington,Skagit County",http://www.wikidata.org/entity/Q113892 +"USA: Washington, Skagit County",http://www.wikidata.org/entity/Q113892 +"USA: Washington,Pierce County",http://www.wikidata.org/entity/Q156459 +"USA: Washington, Pierce County",http://www.wikidata.org/entity/Q156459 +"USA: Washington,Mason County",http://www.wikidata.org/entity/Q111904 +"USA: Washington, Mason County",http://www.wikidata.org/entity/Q111904 +"USA: Washington,Kittitas County",http://www.wikidata.org/entity/Q111540 +"USA: Washington,King County",http://www.wikidata.org/entity/Q108861 +"USA: Washington, King County",http://www.wikidata.org/entity/Q108861 +"USA: King County,WA",http://www.wikidata.org/entity/Q108861 +"USA: Washington,Jefferson County",http://www.wikidata.org/entity/Q384737 +"USA: Washington,Grant County",http://www.wikidata.org/entity/Q281681 +"USA: Washington, Grant County",http://www.wikidata.org/entity/Q281681 +"USA: Washington,Franklin County",http://www.wikidata.org/entity/Q118716 +"USA: Washington, Franklin County",http://www.wikidata.org/entity/Q118716 +"USA: Washington,Clark County",http://www.wikidata.org/entity/Q156287 +"USA: Washington,Benton County",http://www.wikidata.org/entity/Q156216 +"USA: Washington, Benton County",http://www.wikidata.org/entity/Q156216 +"USA: Washington,Asotin County",http://www.wikidata.org/entity/Q156295 +"USA: Washington, Asotin County",http://www.wikidata.org/entity/Q156295 +"USA: Washington,Adams County",http://www.wikidata.org/entity/Q156273 +"USA: Washington, Adams County",http://www.wikidata.org/entity/Q156273 +"USA: Washington, Spokane County",http://www.wikidata.org/entity/Q485276 +"USA: Washington, Douglas County",http://www.wikidata.org/entity/Q156220 +"USA: Washington, Cowlitz County",http://www.wikidata.org/entity/Q156276 USA: TN,http://www.wikidata.org/entity/Q1509 USA: TX,http://www.wikidata.org/entity/Q1439 USA: UT,http://www.wikidata.org/entity/Q829 @@ -347,6 +376,10 @@ 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: Washington,Yakima County",http://www.wikidata.org/entity/Q156629 +"USA: Washington, Yakima County",http://www.wikidata.org/entity/Q156629 +"USA: Washington,Whatcom County",http://www.wikidata.org/entity/Q156623 +"USA: Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200 USA: WV,http://www.wikidata.org/entity/Q1371 USA: WY,http://www.wikidata.org/entity/Q1214 Uzbekistan,http://www.wikidata.org/entity/Q265 diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index bc6ac04..40572a3 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -5,5 +5,6 @@ sapiens,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 +Felis catus; Domestic Shorthair,http://purl.obolibrary.org/obo/NCBITaxon_9685 Panthera tigris jacksoni,http://purl.obolibrary.org/obo/NCBITaxon_419130 Canis lupus familiaris,http://purl.obolibrary.org/obo/NCBITaxon_9615 diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv index 964cbf3..59c4800 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -13,12 +13,14 @@ 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,http://www.ebi.ac.uk/efo/EFO_0008637 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 Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818 Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632 +Oxford Nanopore Sequencing,http://purl.obolibrary.org/obo/NCIT_C146818 MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632 MinION,http://www.ebi.ac.uk/efo/EFO_0008632 Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818 @@ -33,3 +35,24 @@ ThermoFisher S5Plus,http://purl.obolibrary.org/obo/NCIT_C125894 Sanger dideoxy sequencing,http://purl.obolibrary.org/obo/NCIT_C19641 MGISEQ 2000,http://virtual-bh/MGISEQ2000 MGISEQ2000,http://virtual-bh/MGISEQ2000 +Illumina HiSeq X,http://www.ebi.ac.uk/efo/EFO_0008567 +ONT GridION X5,http://www.ebi.ac.uk/efo/EFO_0008633 +ONT PremethION,http://www.ebi.ac.uk/efo/EFO_0008634 +PacBio RS II,http://www.ebi.ac.uk/efo/EFO_0008631 +PacBio Sequel System,http://www.ebi.ac.uk/efo/EFO_0008630 +Illumina Genome Analyzer,http://www.ebi.ac.uk/efo/EFO_0004200 +Illumina Genome Analyzer II,http://www.ebi.ac.uk/efo/EFO_0004201 +Illumina Genome Analyzer IIx,http://www.ebi.ac.uk/efo/EFO_0004202 +454 GS 20 sequencer,http://www.ebi.ac.uk/efo/EFO_0004206 +454 GS FLX Titanium sequencer,http://www.ebi.ac.uk/efo/EFO_0004433 +454 GS FLX sequencer,http://www.ebi.ac.uk/efo/EFO_0004432 +454 GS Junior sequencer,http://www.ebi.ac.uk/efo/EFO_0004434 +454 GS sequencer,http://www.ebi.ac.uk/efo/EFO_0004431 +AB SOLiD 4 System,http://www.ebi.ac.uk/efo/EFO_0004438 +AB SOLiD 4hq System,http://www.ebi.ac.uk/efo/EFO_0004441 +AB SOLiD 5500,http://www.ebi.ac.uk/efo/EFO_0004440 +AB SOLiD 5500xl,http://www.ebi.ac.uk/efo/EFO_0004436 +AB SOLiD PI System,http://www.ebi.ac.uk/efo/EFO_0004437 +AB SOLiD System,http://www.ebi.ac.uk/efo/EFO_0004435 +AB SOLiD System 2.0,http://www.ebi.ac.uk/efo/EFO_0004442 +AB SOLiD System 3.0,http://www.ebi.ac.uk/efo/EFO_0004439 |