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PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#>
PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/>
PREFIX cc: <https://creativecommons.org/ns#>
PREFIX cclicenses: <https://creativecommons.org/licenses/>
PREFIX dc: <http://purl.org/metadata/dublin_core_elements#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
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 CLOSED {
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 CLOSED {
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 CLOSED {
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_~ ] {0,2} ; #(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 CLOSED {
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_C25407 xsd:string ?; #(lab address), Address, optional, string
obo:NCIT_C37900 xsd:string ?; #(provider), Provider, optional, string
obo:NCIT_C164332 xsd:string ?; #(submitter_sample_id), Sample identifier, optional, string
obo:NCIT_C19026 xsd:string ?; #(publication), Scientific Publication, optional string
obo:APOLLO_SV_00000496 /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 CLOSED {
obo:NCIT_C153598 IRI {1,3} ; #(sample_sequencing_technology), DNA Sequencing, mandatory
obo:GENEPIO_0000090 [obo:GENEPIO_0001628 obo:GENEPIO_0002028 ] ; #(assembly method), assembly method, mandatory, one of the two
efo:EFO_0004917 xsd:string ?; #(alignment_protocol), high throughput sequence alignment protocol, 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 CLOSED {
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 CLOSED {
cc:License [ cclicenses:~ ] ;
dc:Title xsd:string ?;
cc:attributionName xsd:string ?;
cc:attributionURL /^http/ ;
cc:attributionSource xsd:string ?;
}
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