diff options
| -rw-r--r-- | bh20sequploader/bh20seq-options.yml | 41 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 8 | ||||
| -rw-r--r-- | bh20sequploader/supporting_webuploader.yml | 48 | ||||
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_countries.csv | 460 | ||||
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv | 2 |
5 files changed, 297 insertions, 262 deletions
diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index d05be5a..da47e1a 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -11,7 +11,40 @@ host_age_unit: Hours: http://purl.obolibrary.org/obo/UO_0000032 host_sex: - Male: http://purl.obolibrary.org/obo/NCIT_C20197 - Female: http://purl.obolibrary.org/obo/NCIT_C27993 - Intersex: http://purl.obolibrary.org/obo/NCIT_C45908 - Unknown: http://purl.obolibrary.org/obo/NCIT_C17998 + Male: http://purl.obolibrary.org/obo/PATO_0000384 + Female: http://purl.obolibrary.org/obo/PATO_0000383 + +sample_sequencing_technology: + Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 + Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566 + Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567 + Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 + Illumina: http://purl.obolibrary.org/obo/OBI_0000759 + IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 + Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 + Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 + Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 + +sample_sequencing_technology2: + Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 + Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566 + Illumina HiSeq X: http://www.ebi.ac.uk/efo/EFO_0008567 + Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 + Illumina: http://purl.obolibrary.org/obo/OBI_0000759 + IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 + Ion Semiconductor Sequencing: http://purl.obolibraryorg/obo/NCIT_C125894 + Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 + Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 + Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 + +specimen_source: + nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 + oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 + sputum: http://purl.obolibrary.org/obo/NCIT_C13278 + bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 + +specimen_source2: + nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 + oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 + sputum: http://purl.obolibrary.org/obo/NCIT_C13278 + bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 4cd0865..fc80080 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -23,15 +23,9 @@ $graph: type: string jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 -# Removed_common_name. Not necessary since we turned species into IRI -# host_common_name: -# doc: Text label for the host species (e.g. homo sapiens) -# type: string? -# jsonldPredicate: -# _id: http://purl.obolibrary.org/obo/NOMEN_0000037 host_sex: doc: Sex of the host as defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown)) - type: string + type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000047 _type: "@id" diff --git a/bh20sequploader/supporting_webuploader.yml b/bh20sequploader/supporting_webuploader.yml deleted file mode 100644 index 3650526..0000000 --- a/bh20sequploader/supporting_webuploader.yml +++ /dev/null @@ -1,48 +0,0 @@ -host_age_unit: - year: http://purl.obolibrary.org/obo/UO_0000036 - month: http://purl.obolibrary.org/obo/UO_0000035 - week: http://purl.obolibrary.org/obo/UO_0000035 - day: http://purl.obolibrary.org/obo/UO_0000034 - hour: http://purl.obolibrary.org/obo/UO_0000032 - -host_sex: - Male: http://purl.obolibrary.org/obo/NCIT_C20197 - Female: http://purl.obolibrary.org/obo/NCIT_C27993 - unknown: http://purl.obolibrary.org/obo/NCIT_C17998 - -sample_sequencing_technology: - Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 - Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 - Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 - IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 - Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 - Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 - -sample_sequencing_technology2: - Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 - Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632 - Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205 - IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894 - Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818 - Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641 - -specimen_source: - nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 - oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 - sputum: http://purl.obolibrary.org/obo/NCIT_C13278 - bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 - -specimen_source2: - nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831 - oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835 - sputum: http://purl.obolibrary.org/obo/NCIT_C13278 - bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195 - -host_species: - OLS-ontology: ncbitaxon - -virus_species: - OLS-ontology: ncbitaxon - -collection_location: - OLS-ontology: gaz
\ No newline at end of file diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 9813f52..a3a55ca 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -1,243 +1,297 @@ -USA,http://www.wikidata.org/entity/Q30 -USA: CA,http://www.wikidata.org/entity/Q99 -USA: ME,http://www.wikidata.org/entity/Q724 -USA: NH,http://www.wikidata.org/entity/Q759 -USA: AL,http://www.wikidata.org/entity/Q173 -USA: MA,http://www.wikidata.org/entity/Q771 -USA: CT,http://www.wikidata.org/entity/Q779 -USA: AK,http://www.wikidata.org/entity/Q797 -USA: HI,http://www.wikidata.org/entity/Q782 -USA: FL,http://www.wikidata.org/entity/Q812 -USA: AZ,http://www.wikidata.org/entity/Q816 -USA: OR,http://www.wikidata.org/entity/Q824 -USA: UT,http://www.wikidata.org/entity/Q829 -USA: MI,http://www.wikidata.org/entity/Q1166 -USA: IL,http://www.wikidata.org/entity/Q1204 -USA: ND,http://www.wikidata.org/entity/Q1207 -USA: SD,http://www.wikidata.org/entity/Q1211 -USA: ID,http://www.wikidata.org/entity/Q1221 -USA: MT,http://www.wikidata.org/entity/Q1212 -USA: WY,http://www.wikidata.org/entity/Q1214 -USA: WA,http://www.wikidata.org/entity/Q1223 -USA: NV,http://www.wikidata.org/entity/Q1227 -USA: CO,http://www.wikidata.org/entity/Q1261 -USA: WV,http://www.wikidata.org/entity/Q1371 -USA: VA,http://www.wikidata.org/entity/Q1370 -USA: RI,http://www.wikidata.org/entity/Q1387 -USA: NY,http://www.wikidata.org/entity/Q1384 -USA: DE,http://www.wikidata.org/entity/Q1393 -USA: OH,http://www.wikidata.org/entity/Q1397 -USA: MD,http://www.wikidata.org/entity/Q1391 -USA: NJ,http://www.wikidata.org/entity/Q1408 -USA: GA,http://www.wikidata.org/entity/Q1428 -USA: PA,http://www.wikidata.org/entity/Q1400 -USA: IN,http://www.wikidata.org/entity/Q1415 -USA: TX,http://www.wikidata.org/entity/Q1439 -USA: NC,http://www.wikidata.org/entity/Q1454 -USA: MS,http://www.wikidata.org/entity/Q1494 -USA: SC,http://www.wikidata.org/entity/Q1456 -USA: NM,http://www.wikidata.org/entity/Q1522 -USA: TN,http://www.wikidata.org/entity/Q1509 -USA: MN,http://www.wikidata.org/entity/Q1527 -USA: WI,http://www.wikidata.org/entity/Q1537 -USA: NE,http://www.wikidata.org/entity/Q1553 -USA: IA,http://www.wikidata.org/entity/Q1546 -USA: OK,http://www.wikidata.org/entity/Q1649 -USA: KS,http://www.wikidata.org/entity/Q1558 -USA: VT,http://www.wikidata.org/entity/Q16551 -USA: MO,http://www.wikidata.org/entity/Q1581 -USA: LA,http://www.wikidata.org/entity/Q1588 -USA: KY,http://www.wikidata.org/entity/Q1603 -USA: AR,http://www.wikidata.org/entity/Q1612 +30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746 +Afghanistan,http://www.wikidata.org/entity/Q889 +Albania,http://www.wikidata.org/entity/Q222 +Algeria,http://www.wikidata.org/entity/Q262 +Andorra,http://www.wikidata.org/entity/Q228 +Angola,http://www.wikidata.org/entity/Q916 +Antigua and Barbuda,http://www.wikidata.org/entity/Q781 +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 +Austria,http://www.wikidata.org/entity/Q40 +Azerbaijan,http://www.wikidata.org/entity/Q227 +Bahrain,http://www.wikidata.org/entity/Q398 +Bangladesh,http://www.wikidata.org/entity/Q902 +Barbados,http://www.wikidata.org/entity/Q244 +Belarus,http://www.wikidata.org/entity/Q184 +Belgium,http://www.wikidata.org/entity/Q31 +Belize,http://www.wikidata.org/entity/Q242 +Benin,http://www.wikidata.org/entity/Q962 +Bhutan,http://www.wikidata.org/entity/Q917 +Bolivia,http://www.wikidata.org/entity/Q750 +Bosnia and Herzegovina,http://www.wikidata.org/entity/Q225 +Botswana,http://www.wikidata.org/entity/Q963 +Brazil,http://www.wikidata.org/entity/Q155 +Brunei,http://www.wikidata.org/entity/Q921 +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 +Cameroon,http://www.wikidata.org/entity/Q1009 +Canada,http://www.wikidata.org/entity/Q16 +Cape Verde,http://www.wikidata.org/entity/Q1011 +Central African Republic,http://www.wikidata.org/entity/Q929 +Chad,http://www.wikidata.org/entity/Q657 +Chile,http://www.wikidata.org/entity/Q298 China,http://www.wikidata.org/entity/Q148 +China: Anhui,http://www.wikidata.org/entity/Q40956 China: Beijing,http://www.wikidata.org/entity/Q956 -China: Hong Kong,http://www.wikidata.org/entity/Q8646 -China: Shanghai,http://www.wikidata.org/entity/Q8686 China: Chongqing,http://www.wikidata.org/entity/Q11725 -China: Tianjin,http://www.wikidata.org/entity/Q11736 -China: Macau,http://www.wikidata.org/entity/Q14773 +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: Guangxi Zhuang Autonomous Region,http://www.wikidata.org/entity/Q15176 -China: Jiangsu,http://www.wikidata.org/entity/Q16963 -China: Zhejiang,http://www.wikidata.org/entity/Q16967 -China: Tibet Autonomous Region,http://www.wikidata.org/entity/Q17269 -China: Heilongjiang,http://www.wikidata.org/entity/Q19206 -China: Sichuan,http://www.wikidata.org/entity/Q19770 -China: Hebei,http://www.wikidata.org/entity/Q21208 -China: Xinjiang,http://www.wikidata.org/entity/Q34800 -China: Anhui,http://www.wikidata.org/entity/Q40956 -China: Inner Mongolia,http://www.wikidata.org/entity/Q41079 -China: Fujian,http://www.wikidata.org/entity/Q41705 +China: Guizhou,http://www.wikidata.org/entity/Q47097 China: Hainan,http://www.wikidata.org/entity/Q42200 -China: Gansu,http://www.wikidata.org/entity/Q42392 -China: Yunnan,http://www.wikidata.org/entity/Q43194 -China: Shandong,http://www.wikidata.org/entity/Q43407 +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: Liaoning,http://www.wikidata.org/entity/Q43934 -China: Jilin,http://www.wikidata.org/entity/Q45208 -China: Hunan,http://www.wikidata.org/entity/Q45761 +China: Hong Kong,http://www.wikidata.org/entity/Q8646 China: Hubei,http://www.wikidata.org/entity/Q46862 -China: Qinghai,http://www.wikidata.org/entity/Q45833 -China: Shanxi,http://www.wikidata.org/entity/Q46913 -China: Shaanxi,http://www.wikidata.org/entity/Q47974 -China: Guizhou,http://www.wikidata.org/entity/Q47097 +"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 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: Ningxia Hui Autonomous Region,http://www.wikidata.org/entity/Q57448 -30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746 -Sri Lanka,http://www.wikidata.org/entity/Q854 -Syria,http://www.wikidata.org/entity/Q858 -Tajikistan,http://www.wikidata.org/entity/Q863 -Canada,http://www.wikidata.org/entity/Q16 -Thailand,http://www.wikidata.org/entity/Q869 -Japan,http://www.wikidata.org/entity/Q17 -Turkmenistan,http://www.wikidata.org/entity/Q874 -Norway,http://www.wikidata.org/entity/Q20 -Ireland,http://www.wikidata.org/entity/Q27 -United Arab Emirates,http://www.wikidata.org/entity/Q878 -Vietnam,http://www.wikidata.org/entity/Q881 -United States of America,http://www.wikidata.org/entity/Q30 -South Korea,http://www.wikidata.org/entity/Q884 +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: Shanxi,http://www.wikidata.org/entity/Q46913 +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: Xinjiang,http://www.wikidata.org/entity/Q34800 +China: Yunnan,http://www.wikidata.org/entity/Q43194 +China: Zhejiang,http://www.wikidata.org/entity/Q16967 +Colombia,http://www.wikidata.org/entity/Q739 +Comoros,http://www.wikidata.org/entity/Q970 +Costa Rica,http://www.wikidata.org/entity/Q800 +Croatia,http://www.wikidata.org/entity/Q224 +Cuba,http://www.wikidata.org/entity/Q241 +Czech Republic,http://www.wikidata.org/entity/Q213 +Democratic Republic of the Congo,http://www.wikidata.org/entity/Q974 Denmark,http://www.wikidata.org/entity/Q35 -Afghanistan,http://www.wikidata.org/entity/Q889 -Bangladesh,http://www.wikidata.org/entity/Q902 -Poland,http://www.wikidata.org/entity/Q36 -Mali,http://www.wikidata.org/entity/Q912 -Italy,http://www.wikidata.org/entity/Q38 -Angola,http://www.wikidata.org/entity/Q916 -Switzerland,http://www.wikidata.org/entity/Q39 -Bhutan,http://www.wikidata.org/entity/Q917 -Austria,http://www.wikidata.org/entity/Q40 -Brunei,http://www.wikidata.org/entity/Q921 -Tanzania,http://www.wikidata.org/entity/Q924 -Turkey,http://www.wikidata.org/entity/Q43 -Philippines,http://www.wikidata.org/entity/Q928 -Portugal,http://www.wikidata.org/entity/Q45 -Uruguay,http://www.wikidata.org/entity/Q77 -Central African Republic,http://www.wikidata.org/entity/Q929 -Togo,http://www.wikidata.org/entity/Q945 +Djibouti,http://www.wikidata.org/entity/Q977 +Dominica,http://www.wikidata.org/entity/Q784 +Dominican Republic,http://www.wikidata.org/entity/Q786 +East Timor,http://www.wikidata.org/entity/Q574 +Ecuador,http://www.wikidata.org/entity/Q736 Egypt,http://www.wikidata.org/entity/Q79 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France,http://www.wikidata.org/entity/Q142 -Comoros,http://www.wikidata.org/entity/Q970 -United Kingdom,http://www.wikidata.org/entity/Q145 -Republic of the Congo,http://www.wikidata.org/entity/Q971 -People's Republic of China,http://www.wikidata.org/entity/Q148 -Democratic Republic of the Congo,http://www.wikidata.org/entity/Q974 -Brazil,http://www.wikidata.org/entity/Q155 -Djibouti,http://www.wikidata.org/entity/Q977 +Gabon,http://www.wikidata.org/entity/Q1000 +Georgia,http://www.wikidata.org/entity/Q230 Germany,http://www.wikidata.org/entity/Q183 -Eritrea,http://www.wikidata.org/entity/Q986 -The Gambia,http://www.wikidata.org/entity/Q1005 -Latvia,http://www.wikidata.org/entity/Q211 -Czech Republic,http://www.wikidata.org/entity/Q213 +Ghana,http://www.wikidata.org/entity/Q117 +Greece,http://www.wikidata.org/entity/Q41 +Grenada,http://www.wikidata.org/entity/Q769 +Guatemala,http://www.wikidata.org/entity/Q774 Guinea,http://www.wikidata.org/entity/Q1006 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\ No newline at end of file +Zambia,http://www.wikidata.org/entity/Q953 +Zimbabwe,http://www.wikidata.org/entity/Q954
\ No newline at end of file diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv index 3ec7e09..12d4e94 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -13,3 +13,5 @@ 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 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 |