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authorlltommy2020-04-19 22:04:27 +0200
committerlltommy2020-04-19 22:04:27 +0200
commita096dbb70e507fb1d2242378a091f1baab645cae (patch)
tree70d6855027999bd0bf92a49023e0e52f965aab34
parent8f97a0e0d8d2d7e32c396d3b9881d770e58ab832 (diff)
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Further updates to our NCBI dictonaries to translate this s*** to our model
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv27
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv6
2 files changed, 28 insertions, 5 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index a3a55ca..79552ed 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -1,4 +1,6 @@
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
Afghanistan,http://www.wikidata.org/entity/Q889
Albania,http://www.wikidata.org/entity/Q222
Algeria,http://www.wikidata.org/entity/Q262
@@ -41,15 +43,18 @@ China: Chongqing,http://www.wikidata.org/entity/Q11725
China: Fujian,http://www.wikidata.org/entity/Q41705
China: Gansu,http://www.wikidata.org/entity/Q42392
China: Guangdong,http://www.wikidata.org/entity/Q15175
+"“China: Guangdong, Guangzhou”",http://www.wikidata.org/entity/Q16572
China: Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176
+China: Guangzhou,http://www.wikidata.org/entity/Q16572
China: Guizhou,http://www.wikidata.org/entity/Q47097
China: Hainan,http://www.wikidata.org/entity/Q42200
China: Hebei,http://www.wikidata.org/entity/Q21208
China: Heilongjiang,http://www.wikidata.org/entity/Q19206
China: Henan,http://www.wikidata.org/entity/Q43684
China: Hong Kong,http://www.wikidata.org/entity/Q8646
+China: HuaShang,http://www.wikidata.org/entity/Q148
China: Hubei,http://www.wikidata.org/entity/Q46862
-"China: Hubei, Wuhan",http://www.wikidata.org/entity/Q11746
+"“China: Hubei, Wuhan”",http://www.wikidata.org/entity/Q11746
China: Hunan,http://www.wikidata.org/entity/Q45761
China: Inner Mongolia,http://www.wikidata.org/entity/Q41079
China: Jiangsu,http://www.wikidata.org/entity/Q16963
@@ -63,13 +68,17 @@ 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: Shanxi,http://www.wikidata.org/entity/Q46913
+China: Shenzhen,http://www.wikidata.org/entity/Q15174
China: Sichuan,http://www.wikidata.org/entity/Q19770
China: Tianjin,http://www.wikidata.org/entity/Q11736
China: Tibet Autonomous Region,http://www.wikidata.org/entity/Q17269
+China: Wuhan,http://www.wikidata.org/entity/Q11746
China: Xinjiang,http://www.wikidata.org/entity/Q34800
China: Yunnan,http://www.wikidata.org/entity/Q43194
China: Zhejiang,http://www.wikidata.org/entity/Q16967
+"“China: Zhejiang, Hangzhou”",http://www.wikidata.org/entity/Q4970
Colombia,http://www.wikidata.org/entity/Q739
+Colombia: Antioquia,http://www.wikidata.org/entity/Q123304
Comoros,http://www.wikidata.org/entity/Q970
Costa Rica,http://www.wikidata.org/entity/Q800
Croatia,http://www.wikidata.org/entity/Q224
@@ -110,8 +119,10 @@ 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: Kerala State,http://www.wikidata.org/entity/Q1186
Indonesia,http://www.wikidata.org/entity/Q252
Iran,http://www.wikidata.org/entity/Q794
+Iran: Qum,http://www.wikidata.org/entity/Q131664
Iran: Tehran,http://www.wikidata.org/entity/Q3616
Iraq,http://www.wikidata.org/entity/Q796
Ireland,http://www.wikidata.org/entity/Q27
@@ -163,12 +174,15 @@ New Zealand,http://www.wikidata.org/entity/Q664
Nicaragua,http://www.wikidata.org/entity/Q811
Niger,http://www.wikidata.org/entity/Q1032
Nigeria,http://www.wikidata.org/entity/Q1033
+Nigeria: Lagos,http://www.wikidata.org/entity/Q8673
North Korea,http://www.wikidata.org/entity/Q423
North Macedonia,http://www.wikidata.org/entity/Q221
Norway,http://www.wikidata.org/entity/Q20
Oman,http://www.wikidata.org/entity/Q842
Ottoman Empire,http://www.wikidata.org/entity/Q12560
Pakistan,http://www.wikidata.org/entity/Q843
+Pakistan: Gilgit,http://www.wikidata.org/entity/Q609024
+Pakistan: KPK,http://www.wikidata.org/entity/Q183314
Palau,http://www.wikidata.org/entity/Q695
Panama,http://www.wikidata.org/entity/Q804
Papua New Guinea,http://www.wikidata.org/entity/Q691
@@ -203,6 +217,7 @@ Slovenia,http://www.wikidata.org/entity/Q215
Solomon Islands,http://www.wikidata.org/entity/Q685
Somalia,http://www.wikidata.org/entity/Q1045
South Africa,http://www.wikidata.org/entity/Q258
+South Africa: KwaZulu-Natal,http://www.wikidata.org/entity/Q81725
South African Republic,http://www.wikidata.org/entity/Q550374
South Korea,http://www.wikidata.org/entity/Q884
South Sudan,http://www.wikidata.org/entity/Q958
@@ -215,6 +230,7 @@ Suriname,http://www.wikidata.org/entity/Q730
Sweden,http://www.wikidata.org/entity/Q34
Switzerland,http://www.wikidata.org/entity/Q39
Syria,http://www.wikidata.org/entity/Q858
+Taiwan,http://www.wikidata.org/entity/Q865
Tajikistan,http://www.wikidata.org/entity/Q863
Tanzania,http://www.wikidata.org/entity/Q924
Thailand,http://www.wikidata.org/entity/Q869
@@ -224,6 +240,7 @@ Togo,http://www.wikidata.org/entity/Q945
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
Turkey,http://www.wikidata.org/entity/Q43
Turkmenistan,http://www.wikidata.org/entity/Q874
Tuvalu,http://www.wikidata.org/entity/Q672
@@ -240,6 +257,7 @@ 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: CA,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: DE,http://www.wikidata.org/entity/Q1393
@@ -249,6 +267,7 @@ USA: HI,http://www.wikidata.org/entity/Q782
USA: IA,http://www.wikidata.org/entity/Q1546
USA: ID,http://www.wikidata.org/entity/Q1221
USA: IL,http://www.wikidata.org/entity/Q1204
+USA: Illinois,http://www.wikidata.org/entity/Q1204
USA: IN,http://www.wikidata.org/entity/Q1415
USA: KS,http://www.wikidata.org/entity/Q1558
USA: KY,http://www.wikidata.org/entity/Q1603
@@ -274,6 +293,7 @@ USA: OK,http://www.wikidata.org/entity/Q1649
USA: OR,http://www.wikidata.org/entity/Q824
USA: PA,http://www.wikidata.org/entity/Q1400
USA: RI,http://www.wikidata.org/entity/Q1387
+"“USA: San Francisco, CA”",http://www.wikidata.org/entity/Q62
USA: SC,http://www.wikidata.org/entity/Q1456
USA: SD,http://www.wikidata.org/entity/Q1211
USA: TN,http://www.wikidata.org/entity/Q1509
@@ -289,9 +309,10 @@ Uzbekistan,http://www.wikidata.org/entity/Q265
Vanuatu,http://www.wikidata.org/entity/Q686
Vatican City,http://www.wikidata.org/entity/Q237
Venezuela,http://www.wikidata.org/entity/Q717
-Vietnam,http://www.wikidata.org/entity/Q881
Viet nam,http://www.wikidata.org/entity/Q881
+Viet Nam,http://www.wikidata.org/entity/Q881
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 12d4e94..8e37b8c 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -5,6 +5,7 @@ Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
ONT (Oxford Nanopore Technologies),http://www.ebi.ac.uk/efo/EFO_0008632
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
Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205
Illumina,http://purl.obolibrary.org/obo/OBI_0000759
Oxford Nanopore technology,http://purl.obolibrary.org/obo/NCIT_C146818
@@ -12,6 +13,7 @@ Oxford Nanopore Technologies,http://purl.obolibrary.org/obo/NCIT_C146818
Oxford Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818
IonTorrent,http://purl.obolibrary.org/obo/NCIT_C125894
Ion Torrent X5Plus,http://purl.obolibrary.org/obo/NCIT_C125894
+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 \ No newline at end of file
+MGISEQ 2000,http://virtual-bh/MGISEQ2000
+MGISEQ2000,http://virtual-bh/MGISEQ2000 \ No newline at end of file