PREFIX : PREFIX MainSchema: PREFIX hostSchema: PREFIX cc: PREFIX cclicenses: PREFIX dc: PREFIX xsd: PREFIX obo: PREFIX sio: PREFIX efo: PREFIX evs: PREFIX edam: PREFIX wikidata: :submissionShape { MainSchema:host @:hostShape ; MainSchema:sample @:sampleShape ; MainSchema:submitter @:submitterShape ; MainSchema:technology @:technologyShape ; MainSchema:virus @:virusShape; 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_~ ] ; #(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; #(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 + ; #(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 {1,3} ; #(sample_sequencing_technology), sequencing assay, optional efo:EFO_0004917 xsd:string ; #(alignment_protocol), high throughput sequence alignment protocol, optional obo:GENEPIO_0000090 [obo:GENEPIO_0001628 obo:GENEPIO_0002028 ] ? ; #(assembly method), assembly method, optional, one of the two 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_~ ] ; # (virus_species) NCBI taxon, mandatory, from namespace obo:NCBITaxon_ sio:SIO_010055 xsd:string ?; # (virus_strain) strain, optional string } :licenseShape{ cc:License [ cclicenses:~ ] ; dc:Title xsd:string ?; cc:attributionName xsd:string ?; cc:attributionURL /^http/ ; cc:attributionSource xsd:string ?; }