aboutsummaryrefslogtreecommitdiff
path: root/scripts/dict_ontology_standardization
diff options
context:
space:
mode:
Diffstat (limited to 'scripts/dict_ontology_standardization')
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv29
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv6
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv3
3 files changed, 34 insertions, 4 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index a3a55ca..d5e2235 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
@@ -9,6 +11,7 @@ Argentina,http://www.wikidata.org/entity/Q414
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
Austria,http://www.wikidata.org/entity/Q40
Azerbaijan,http://www.wikidata.org/entity/Q227
Bahrain,http://www.wikidata.org/entity/Q398
@@ -41,13 +44,16 @@ 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: Hunan,http://www.wikidata.org/entity/Q45761
@@ -63,13 +69,18 @@ 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: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 +121,10 @@ 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 +176,15 @@ 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 +219,7 @@ 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 +232,7 @@ 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 +242,7 @@ 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 +259,7 @@ 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 +269,7 @@ 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
@@ -267,6 +288,7 @@ USA: NE,http://www.wikidata.org/entity/Q1553
USA: NH,http://www.wikidata.org/entity/Q759
USA: NJ,http://www.wikidata.org/entity/Q1408
USA: NM,http://www.wikidata.org/entity/Q1522
+USA: North Carolina,http://www.wikidata.org/entity/Q1454
USA: NV,http://www.wikidata.org/entity/Q1227
USA: NY,http://www.wikidata.org/entity/Q1384
USA: OH,http://www.wikidata.org/entity/Q1397
@@ -274,8 +296,10 @@ 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: Snohomish County, WA",http://www.wikidata.org/entity/Q110403
USA: TN,http://www.wikidata.org/entity/Q1509
USA: TX,http://www.wikidata.org/entity/Q1439
USA: UT,http://www.wikidata.org/entity/Q829
@@ -289,9 +313,10 @@ 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
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index fcd6c94..2905588 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -20,3 +20,6 @@ swab,http://purl.obolibrary.org/obo/NCIT_C13195
oral swab,http://purl.obolibrary.org/obo/NCIT_C13195
bronchoalveolar lavage,http://purl.obolibrary.org/obo/NCIT_C13195
sputum,http://purl.obolibrary.org/obo/NCIT_C13278
+aspirate,http://purl.obolibrary.org/obo/NCIT_C13347
+stool,http://purl.obolibrary.org/obo/NCIT_C13234
+serum,http://purl.obolibrary.org/obo/NCIT_C13325 \ No newline at end of file