diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 73 |
1 files changed, 38 insertions, 35 deletions
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 11eb75e..6e2493b 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -21,54 +21,57 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> MainSchema:license @:licenseShape ?; } +## documentation: #(name of option in yaml), ontology label, mandatory|optional, type +## entries marked with ?????? need review + :hostShape { - efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; - sio:SIO_000115 xsd:string ?; - obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?; - obo:PATO_0000011 xsd:integer ?; - obo:NCIT_C42574 [ obo:UO_~ ] ?; - obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ; - efo:EFO_0000727 xsd:string ?; - obo:VO_0000002 xsd:string {0,10}; - sio:SIO_001167 xsd:string ?; - sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #ethnicity from obo:HANCESTRO + efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; #(host_species host), mandatory field, from namespace obo:NCBITaxon + sio:SIO_000115 xsd:string ?; #(host_id), identifier, optional string + obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 obo:PATO_0001340] ?; #(host_sex) biological sex, optional, one selected value + obo:PATO_0000011 xsd:integer ?; #(host_age) age, optional integer + obo:NCIT_C42574 [ obo:UO_~ ] ?; #host_age_unit, optional from namespace obo:UO + obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ; #(host_health_status) status, optional, one selected value + efo:EFO_0000727 xsd:string ?; #(host_treatment), treatment, optional + obo:VO_0000002 xsd:string {0,10}; #(host_vaccination), vaccination, optional list of String 0-10 + sio:SIO_001014 [ obo:HANCESTRO_~ ] ? ; #(ethnicity), ethnicity from obo:HANCESTRO + sio:SIO_001167 xsd:string ?; #(additional_host_information), comment, optional, string } :sampleShape { - sio:SIO_000115 xsd:string; - evs:C25164 xsd:string; - obo:GAZ_00000448 [wikidata:~] ; - obo:OBI_0001895 xsd:string ?; - obo:NCIT_C41206 xsd:string ?; - obo:OBI_000147 [ obo:NCIT_~ ] ? ; #specimen source from obo:NCIT - obo:OBI_0001472 xsd:string ?; - sio:SIO_001167 xsd:string ?; - edam:data_2091 IRI {0,3}; + sio:SIO_000115 xsd:string; #(sampleId), identifier, mandatory string + evs:C25164 xsd:string; #(collection_date), date, mandatory, string but should be date + obo:GAZ_00000448 [wikidata:~] ; #(collection_location), geographic location, mandatory, from wikidata namespace + obo:OBI_0001895 xsd:string ?; #(collector_name), specimen collector, optional string + obo:NCIT_C41206 xsd:string ?; #(collecting_institution) Institute, optional string + obo:OBI_0001479 [ obo:NCIT_~ ] ? ; #(specimen_source), specimen from organism, optional, from obo:NCIT + obo:OBI_0001472 xsd:string ?; #(sample_storage_conditions), specimen with known storage state, optional string + sio:SIO_001167 xsd:string ?; #(additional_collection_information), comment, optional, string + edam:data_2091 IRI {0,3}; #(source_database_accession), Accession, optional, IRI 0-3 } :submitterShape { - obo:NCIT_C42781 xsd:string + ; - sio:SIO_000116 xsd:string *; - sio:SIO_000172 xsd:string ?; - obo:NCIT_C37984 xsd:string ?; - obo:NCIT_C37900 xsd:string ?; - efo:EFO_0001741 xsd:string ?; - obo:NCIT_C42781 xsd:string ?; - obo:NCIT_C19026 xsd:string ?; - sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10}; - sio:SIO_001167 xsd:string ?; + obo:NCIT_C42781 xsd:string + ; #(authors), Author, mandatory, list 1-* + sio:SIO_000116 xsd:string *; #(submitter_name), name, optional 0-* + sio:SIO_000172 xsd:string ?; #(submitter_address), address, optional, string + obo:NCIT_C37984 xsd:string ?; #(originating_lab) Laboratory, optional, string + obo:NCIT_C37900 xsd:string ?; #(lab address), Provider, optional, string + efo:EFO_0001741 xsd:string ?; #(provider_sample_id), submitter, optional ???????????????????? + obo:NCIT_C42781 xsd:string ?; #(submitter_sample_id), Author, optional string ???????????????????? + obo:NCIT_C19026 xsd:string ?; #(publication), Scientific Publication, optional string + sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/ {0,10}; #(submitter_orcid) identifier, optional but given regular expression + sio:SIO_001167 xsd:string ?; #(additional_submitter_information), comment, optional string } :technologyShape { - obo:OBI_0600047 IRI {0,3} ; - efo:EFO_0002699 xsd:string ?; - obo:FLU_0000848 xsd:double OR xsd:integer {0,3}; - sio:SIO_001167 xsd:string ?; + obo:OBI_0600047 IRI {0,3} ; #(sample_sequencing_technology) sequencing assay, optional ???????????? + efo:EFO_0002699 xsd:string ?; #(sequence_assembly_method) high throughput sequencer, optional ????????????? + obo:FLU_0000848 xsd:double OR xsd:integer {0,3}; #(sequence coverage) sequence coverage, optional + sio:SIO_001167 xsd:string ?; #(additional_technology_information), comment, optional, string } :virusShape{ - edam:data_1875 [ obo:NCBITaxon_~ ] ; - sio:SIO_010055 xsd:string ?; + edam:data_1875 [ obo:NCBITaxon_~ ] ; # (virus_species) NCBI taxon, mandatory, from namespace obo:NCBITaxon_ + sio:SIO_010055 xsd:string ?; # (virus_strain) strain, optional string } :licenseShape{ |