Hts - xiaofengleo/phenopackets-rdf-schema GitHub Wiki

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.

Semantic model figure

---

ShEx

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	
}

---

Example turtle

@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:NCIT_C43412.

:distribution1 a dcat:Distribution;
    sio:SIO_001403 :sample1; # associated with
    dct:description "Matched normal germline sample";
    dcat:downloadURL <https://opensnp.org/data/60.23andme-exome-vcf.231?1341012444>;
    dct:format <http://edamontology.org/format_3016> .

:genomeAssembly1 a obo:SO_0001505;
  sio:SIO_001403 <https://opensnp.org/data/60.23andme-exome-vcf.231?1341012444>;
  rdfs:label "GRCh38" .