diff options
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 6 | ||||
| -rw-r--r-- | example/metadata.yaml | 4 | ||||
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_countries.csv | 14 | ||||
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_speciesman_source.csv | 3 |
4 files changed, 19 insertions, 8 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index c48ebce..5000f08 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -78,11 +78,13 @@ $graph: type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 + _type: "@id" specimen_source2: doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155835 (=throat swabb) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 + _type: "@id" collection_date: doc: Date when the sample was taken type: string? @@ -95,7 +97,7 @@ $graph: _id: http://purl.obolibrary.org/obo/GAZ_00000448 _type: "@id" sample_storage_conditions: - doc: Information aboout storage of a specified type, e.g. frozen specimen, paraffin, fresh .... + doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh .... type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001472 @@ -138,11 +140,13 @@ $graph: type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 + _type: "@id" sample_sequencing_technology2: doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 + _type: "@id" sequence_assembly_method: doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome type: string? diff --git a/example/metadata.yaml b/example/metadata.yaml index 5e1be0a..1e7f29c 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -15,8 +15,8 @@ sample: sample_id: Id of the sample as defined by the submitter collector_name: Name of the person that took the sample collecting_institution: Institute that was responsible of sampeling - specimen_source: Method how specimen was derived - specimen_source2: Method how specimen was derived if two methods were used + specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831 + specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835 collection_date: Date when the sample was taken collection_location: http://www.wikidata.org/entity/Q148 sample_storage_conditions: XXX diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 79552ed..d5e2235 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -11,6 +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 @@ -43,7 +44,7 @@ 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: 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 @@ -54,7 +55,7 @@ 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 @@ -73,10 +74,11 @@ 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 +"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 @@ -257,7 +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: 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 @@ -286,6 +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 @@ -293,9 +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: 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 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
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