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-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv35
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv13
2 files changed, 43 insertions, 5 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 2599b62..618e3e1 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -1,6 +1,20 @@
30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746
35.92 N 74.33 E,http://www.wikidata.org/entity/Q609024
39.54 N 116.23 E,http://www.wikidata.org/entity/Q198244
+22.3039019 N 73.1680977 E,http://www.wikidata.org/entity/Q11909
+22.3394 N 114.166 E,http://www.wikidata.org/entity/Q8646
+22.6813385 N 72.8771793 E,http://www.wikidata.org/entity/Q219039
+23.052214 N 72.603157 E,http://www.wikidata.org/entity/Q1070
+23.0524508 N 72.600668 E,http://www.wikidata.org/entity/Q1070
+24.5046286 N 72.0209126 E,http://www.wikidata.org/entity/Q1266017
+40.71 N 74.00 W,http://www.wikidata.org/entity/Q11253
+41.31 N 72.92 W,http://www.wikidata.org/entity/Q49145
+43.0731 N 89.4012 W,http://www.wikidata.org/entity/Q43788
+44.3148 N 85.6024 W,http://www.wikidata.org/entity/Q22086086
+51.06 N 6.12 E,http://www.wikidata.org/entity/Q14833
+51.22 N 6.77 E,http://www.wikidata.org/entity/Q1718
+22.3137564 N 73.1465874 E,http://www.wikidata.org/entity/Q11909
+"22.8197678 N 72.7573375 E",http://www.wikidata.org/entity/Q2233469
Afghanistan,http://www.wikidata.org/entity/Q889
Albania,http://www.wikidata.org/entity/Q222
Algeria,http://www.wikidata.org/entity/Q262
@@ -237,11 +251,11 @@ India:Kerala State,http://www.wikidata.org/entity/Q1186
"India:Vadodara",http://www.wikidata.org/entity/Q11909
"India:Gujarat, Vadodara",http://www.wikidata.org/entity/Q11909
"India:Hyderabad",http://www.wikidata.org/entity/Q1361
-"India:hamadan",http://www.wikidata.org/entity/Q1361
-"India:Hamadan",http://www.wikidata.org/entity/Q28587
+"Iran:hamadan",http://www.wikidata.org/entity/Q1361
+"Iran:Hamadan",http://www.wikidata.org/entity/Q28587
"Iraq:Erbil",http://www.wikidata.org/entity/Q132754
"Iraq:Kurdistan region, Erbil",http://www.wikidata.org/entity/Q132754
-"Iraq:Kurdistan region, Erbil",http://www.wikidata.org/entity/Q132754
+"Iraq:Kuedistan region, Erbil",http://www.wikidata.org/entity/Q132754
Indonesia,http://www.wikidata.org/entity/Q252
Iran,http://www.wikidata.org/entity/Q794
Iran:Qum,http://www.wikidata.org/entity/Q131664
@@ -294,6 +308,7 @@ Mauritania,http://www.wikidata.org/entity/Q1025
Mauritius,http://www.wikidata.org/entity/Q1027
Mexico,http://www.wikidata.org/entity/Q96
Mexico:Baja California Sur,http://www.wikidata.org/entity/Q46508
+"Mexico:Tijuana, BajaCalifornia",http://www.wikidata.org/entity/Q124739
Mexico:Hidalgo,http://www.wikidata.org/entity/Q80903
Mexico:Mexico City,http://www.wikidata.org/entity/Q1489
Mexico:Mexico State,http://www.wikidata.org/entity/Q82112
@@ -409,6 +424,8 @@ Tonga,http://www.wikidata.org/entity/Q678
Trinidad and Tobago,http://www.wikidata.org/entity/Q754
Tunisia,http://www.wikidata.org/entity/Q948
Tunisia:Tunis,http://www.wikidata.org/entity/Q3572
+Tunisia:Ben Arous,http://www.wikidata.org/entity/Q816443
+Tunisia:Bizerte,http://www.wikidata.org/entity/Q189546
Turkey,http://www.wikidata.org/entity/Q43
Turkmenistan,http://www.wikidata.org/entity/Q874
Tuvalu,http://www.wikidata.org/entity/Q672
@@ -428,11 +445,13 @@ USA:AL,http://www.wikidata.org/entity/Q173
"USA:Alabama",http://www.wikidata.org/entity/Q173
"USA:Alabama, Mobile county",http://www.wikidata.org/entity/Q495738
"USA:Arizona, Maricopa county",http://www.wikidata.org/entity/Q58691
+"USA:Maricopa County, Arizona",http://www.wikidata.org/entity/Q58691
"USA:Arkansas, Little Rock",http://www.wikidata.org/entity/Q33405
"USA:Avondale, LA",http://www.wikidata.org/entity/Q79449
"USA:AVONDALE, LA",http://www.wikidata.org/entity/Q79449
"USA:CA, Alameda",http://www.wikidata.org/entity/Q490744
"USA:California, Los Angeles county",http://www.wikidata.org/entity/Q104994
+"USA:California,Los Angeles County",http://www.wikidata.org/entity/Q104994
"USA:California, San Diego county",http://www.wikidata.org/entity/Q108143
"USA:California, Santa Clara county",http://www.wikidata.org/entity/Q110739
"USA:Colorado, Denver county",http://www.wikidata.org/entity/Q15906757
@@ -455,6 +474,7 @@ USA:AL,http://www.wikidata.org/entity/Q173
"USA:Illinois, Winnebago county",http://www.wikidata.org/entity/Q110606
"USA:Illinois, Winnebago County",http://www.wikidata.org/entity/Q110606
"USA:Imperial, California",http://www.wikidata.org/entity/Q169952
+"USA:South Carolina, Fairfield",http://www.wikidata.org/entity/Q323432
"USA:Iowa, Dubuque county",http://www.wikidata.org/entity/Q113756
"USA:Iowa, Jackson county",http://www.wikidata.org/entity/Q485780
"USA:Killona, LA",http://www.wikidata.org/entity/Q1844136
@@ -508,18 +528,22 @@ USA:New Hampshire,http://www.wikidata.org/entity/Q759
"USA:Wisconsin, Dane county",http://www.wikidata.org/entity/Q502200
"USA:Wisconsin, Dane County",http://www.wikidata.org/entity/Q502200
"USA:Wisconsin, Dodge County",http://www.wikidata.org/entity/Q372796
+"USA:Wisconsin, Dodge county",http://www.wikidata.org/entity/Q372796
"USA:Wisconsin, Fond du Lac county",http://www.wikidata.org/entity/Q494912
"USA:Wisconsin, Grant county",http://www.wikidata.org/entity/Q500977
"USA:Wisconsin, Green county",http://www.wikidata.org/entity/Q489163
"USA:Wisconsin, Jackson county",http://www.wikidata.org/entity/Q500897
+"USA:Wisconsin, Jefferson county",http://www.wikidata.org/entity/Q500958
"USA:Wisconsin, Lafayette county",http://www.wikidata.org/entity/Q431440
"USA:Wisconsin, Manitowoc county",http://www.wikidata.org/entity/Q500984
+"USA:Wisconsin, Marquette county",http://www.wikidata.org/entity/Q500918
"USA:Wisconsin, Milwaukee county",http://www.wikidata.org/entity/Q502294
"USA:Wisconsin, Monroe county",http://www.wikidata.org/entity/Q932966
"USA:Wisconsin, Outagamie county",http://www.wikidata.org/entity/Q510244
"USA:Wisconsin, Ozaukee county",http://www.wikidata.org/entity/Q505874
"USA:Wisconsin, Racine county",http://www.wikidata.org/entity/Q510122
"USA:Wisconsin, Richland county",http://www.wikidata.org/entity/Q501596
+"USA:Wisconsin, Rock county",http://www.wikidata.org/entity/Q500939
"USA:Wisconsin, Sauk county",http://www.wikidata.org/entity/Q500933
"USA:Wisconsin, Sheboygan county",http://www.wikidata.org/entity/Q500803
"USA:Wisconsin, Trempealeau county",http://www.wikidata.org/entity/Q494923
@@ -587,8 +611,8 @@ USA:KS,http://www.wikidata.org/entity/Q1558
USA:KY,http://www.wikidata.org/entity/Q1603
USA:LA,http://www.wikidata.org/entity/Q65
USA:Los Angeles,http://www.wikidata.org/entity/Q65
-"USA:SLIDELL, LA, LA",https://www.wikidata.org/wiki/Q988156
-"USA:Slidell, LA, LA",https://www.wikidata.org/wiki/Q988156
+"USA:SLIDELL, LA",https://www.wikidata.org/wiki/Q988156
+"USA:Slidell, LA",https://www.wikidata.org/wiki/Q988156
"USA:Seattle, WA",https://www.wikidata.org/wiki/Q5083
"USA:New Orleans, LA",https://www.wikidata.org/wiki/Q34404
"USA:NEW ORLEANS, LA",https://www.wikidata.org/wiki/Q34404
@@ -647,6 +671,7 @@ USA:SD,http://www.wikidata.org/entity/Q1211
"USA:King County,WA",http://www.wikidata.org/entity/Q108861
"USA:Washington,Jefferson County",http://www.wikidata.org/entity/Q384737
"USA:Washington, Jefferson County",http://www.wikidata.org/entity/Q384737
+"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
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index 0fa2219..42168e6 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -1,14 +1,23 @@
nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+Nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+NPS,http://purl.obolibrary.org/obo/NCIT_C155831
+NasopharyngealSwab,http://purl.obolibrary.org/obo/NCIT_C155831
+Naso-pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharingeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+Nasopharyngeal (NP) 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
+Nasopharyngeal,http://purl.obolibrary.org/obo/NCIT_C155831
respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831
naso-pharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
nasopharyngeal aspirate,http://purl.obolibrary.org/obo/NCIT_C155831
nasal swab specimen,http://purl.obolibrary.org/obo/NCIT_C155831
+nasal swal,http://purl.obolibrary.org/obo/NCIT_C155831
pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
respiratory secretion,http://purl.obolibrary.org/obo/NCIT_C155831
mid-nasal swab,http://purl.obolibrary.org/obo/NCIT_C155831
+Mid-nasal swab,http://purl.obolibrary.org/obo/NCIT_C155831
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
@@ -16,7 +25,10 @@ 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
+oral-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
+oro-pharngyl swab,http://purl.obolibrary.org/obo/NCIT_C155835
Oro-pharyngeal swab,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
@@ -33,4 +45,5 @@ aspirate,http://purl.obolibrary.org/obo/NCIT_C13347
stool,http://purl.obolibrary.org/obo/NCIT_C13234
serum,http://purl.obolibrary.org/obo/NCIT_C13325
saliva,http://purl.obolibrary.org/obo/NCIT_C13275
+Deep throat saliva,http://purl.obolibrary.org/obo/NCIT_C13275
nasal swab,http://purl.obolibrary.org/obo/NCIT_C132119