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Hts
Rajaram edited this page Sep 7, 2021
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We used Data Catalog Vocabulary to describe the fields of HtsFile. We used generic sio:is associated with
predicate to connect Sample
and genome assembly
used in the HtSFile.
@prefix : <http://purl.org/ejp-rd/phenopackets-rdf-schema/v010/example-rdf/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
:sample1 a obo:OBI_0100051. # specimen
:distribution1 a dcat:Distribution;
sio:SIO_001403 :sample1; # associated with
dct:description "Matched normal germline sample";
dcat:downloadURL <https://example.com/some-vcf>;
dct:format <http://edamontology.org/format_3016> .
:genomeAssembly1 a obo:SO_0001505;
sio:SIO_001403 <https://example.com/some-vcf>;
rdfs:label "GRCh38" .
PREFIX : <http://purl.org/ejp-rd/phenopackets-rdf-schema/v010/shex/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX dcat: <http://www.w3.org/ns/dcat#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX edam: <http://edamontology.org/>
PREFIX phenordf: <http://purl.org/ejp-rd/phenopackets-rdf-schema/resources/rdf/>
:sampleShape IRI {
a [obo:NCIT_C43412]
}
:distributionShape IRI {
a [dcat:Distribution];
sio:SIO_001403 @:sampleShape;
dct:description xsd:string;
dcat:downloadURL @:downloadShape;
dct:format [edam:format_2573 edam:format_2572 edam:format_3462 edam:format_3016 edam:format_3020 :gvcf edam:format_1930] # SAM, BAM, CRAM, VCF, BCF, GVCF, FASTQ
}
:downloadShape IRI {
}
:genomeAssemblyShape IRI {
a [obo:SO_0001505];
sio:SIO_001403 @:downloadShape;
rdfs:label xsd:string
}