diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 52 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 25 |
2 files changed, 38 insertions, 39 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 982447c..3d8604a 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -21,7 +21,7 @@ $graph: identity: true host_id: doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples - type: string + type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 host_sex: @@ -66,16 +66,27 @@ $graph: - name: sampleSchema type: record fields: + collection_date: + doc: Date when the sample was taken + type: string + jsonldPredicate: + _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 + collection_location: + doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China) + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/GAZ_00000448 + _type: "@id" collector_name: doc: Name of the person that took the sample - type: string + type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001895 collecting_institution: doc: Institute that was responsible of sampeling - type: string + type: string? jsonldPredicate: - _id: http://semanticscience.org/resource/SIO_001167 + _id: http://purl.obolibrary.org/obo/NCIT_C41206 specimen_source: doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab) type: string? @@ -89,19 +100,6 @@ $graph: jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 _type: "@id" - identity: true - collection_date: - doc: Date when the sample was taken - type: string - jsonldPredicate: - _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 - collection_location: - doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China) - type: string - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/GAZ_00000448 - _type: "@id" - identity: true sample_storage_conditions: doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh .... type: string? @@ -114,7 +112,7 @@ $graph: _id: http://semanticscience.org/resource/SIO_001167 sample_id: doc: Id of the sample as defined by the submitter - type: string + type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 source_database_accession: @@ -167,7 +165,7 @@ $graph: jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 sequencing_coverage2: - doc: If a second sequence technology was use you can submit its coverage here + doc: If a second sequence technology was used you can submit its coverage here type: float? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 @@ -180,9 +178,14 @@ $graph: - name: submitterSchema type: record fields: + authors: + doc: Name of the author(s) + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C42781 submitter_name: doc: Name of the submitter - type: string + type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000116 submitter_address: @@ -192,7 +195,7 @@ $graph: _id: http://semanticscience.org/resource/SIO_000172 originating_lab: doc: Name of the laboratory that took the sample - type: string + type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C37984 lab_address: @@ -208,11 +211,6 @@ $graph: type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0001741 - authors: - doc: Name of the author(s) - type: string? - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/NCIT_C42781 publication: doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...) type: string? @@ -232,7 +230,7 @@ $graph: fields: host: hostSchema sample: sampleSchema - virus: virusSchema? + virus: virusSchema technology: technologySchema submitter: submitterSchema id: diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 8d3f5fc..6e646c7 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -7,6 +7,7 @@ PREFIX sio: <http://semanticscience.org/resource/> PREFIX efo: <http://www.ebi.ac.uk/efo/> PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> PREFIX edam: <http://edamontology.org/> +PREFIX wikidata: <http://www.wikidata.org/entity/> :submissionShape { MainSchema:host @:hostShape ; @@ -18,8 +19,8 @@ PREFIX edam: <http://edamontology.org/> :hostShape { efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; - obo:PATO_0000047 [ obo:NCIT_C20197 obo:NCIT_C27993 obo:NCIT_C17998 ] ; - sio:SIO_000115 xsd:string ; + sio:SIO_000115 xsd:string ?; + obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?; obo:PATO_0000011 xsd:integer ?; obo:NCIT_C42574 [ obo:UO_~ ] ?; sio:SIO_001167 xsd:string ?; @@ -27,20 +28,20 @@ PREFIX edam: <http://edamontology.org/> } :sampleShape { - obo:OBI_0001895 xsd:string ; - sio:SIO_000115 xsd:string ; - sio:SIO_001167 xsd:string ; - evs:C25164 xsd:string ?; - obo:GAZ_00000448 [obo:GAZ_~] ?; + evs:C25164 xsd:string?; + obo:GAZ_00000448 [wikidata:~] ; + obo:OBI_0001895 xsd:string ?; + sio:SIO_001167 xsd:string ?; + sio:SIO_000115 xsd:string ?; obo:OBI_0001472 xsd:string ?; - obo:OBI_0001479 xsd:string ?; + obo:OBI_0001479 IRI {0,2}; } :submitterShape { - sio:SIO_000116 xsd:string ; - obo:NCIT_C37984 xsd:string ; + obo:NCIT_C42781 xsd:string ; + obo:NCIT_C37984 xsd:string ?; obo:NCIT_C37900 xsd:string ?; - obo:NCIT_C42781 xsd:string ?; + sio:SIO_000116 xsd:string ?; obo:OBI_0600047 xsd:string ?; sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?; sio:SIO_000172 xsd:string ?; @@ -48,7 +49,7 @@ PREFIX edam: <http://edamontology.org/> } :technologyShape { - obo:OBI_0600047 xsd:string ; + obo:OBI_0600047 IRI {0,2} ; obo:FLU_0000848 xsd:integer ?; efo:EFO_0002699 xsd:string ?; } |