{ "resourceType": "StructureDefinition", "id": "HtsFile", "meta": { "lastUpdated": "2019-12-20T21:24:38.253+00:00" }, "text": { "status": "generated", "div": "
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\"DocumentReference0..*DocumentReference
\".\"\".\"\".\"extension0..*ExtensionSlice: Unordered, Open by value:url
\".\"\".\"\".\"htsfile-genome-assemblyS1..1stringThe genome assembly the contents of this file was called against.
URL: http://ga4gh.org/fhir/phenopackets/StructureDefinition/htsfile-genome-assembly
\".\"\".\"\".\"statusS1..1codeFixed Value: current
\".\"\".\"\".\"typeS1..1CodeableConceptBinding: HTS Format (required)
\".\"\".\"\".\"subjectS0..1Reference(Phenopacket | Cohort | Family)

\"doco\" Documentation for this format
" }, "url": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/HtsFile", "version": "0.1.0", "name": "HtsFile", "title": "Hts File", "status": "draft", "date": "2019-12-20T18:15:04+00:00", "publisher": "Global Alliance for Genomics and Health", "contact": [ { "telecom": [ { "system": "other", "value": "http://ga4gh.org", "rank": 1 } ] } ], "description": "Phenopackets can be used to hold phenotypic information that can inform the analysis of sequencing data in VCF format as well as other high-throughput sequencing (HTS) or other data types.", "fhirVersion": "4.0.1", "mapping": [ { "identity": "workflow", "uri": "http://hl7.org/fhir/workflow", "name": "Workflow Pattern" }, { "identity": "fhircomposition", "uri": "http://hl7.org/fhir/composition", "name": "FHIR Composition" }, { "identity": "rim", "uri": "http://hl7.org/v3", "name": "RIM Mapping" }, { "identity": "cda", "uri": "http://hl7.org/v3/cda", "name": "CDA (R2)" }, { "identity": "w5", "uri": "http://hl7.org/fhir/fivews", "name": "FiveWs Pattern Mapping" }, { "identity": "v2", "uri": "http://hl7.org/v2", "name": "HL7 v2 Mapping" }, { "identity": "xds", "uri": "http://ihe.net/xds", "name": "XDS metadata equivalent" } ], "kind": "resource", "abstract": false, "type": "DocumentReference", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/DocumentReference", "derivation": "constraint", "snapshot": {}, "differential": { "element": [ { "id": "DocumentReference", "path": "DocumentReference" }, { "id": "DocumentReference.extension", "path": "DocumentReference.extension", "slicing": { "discriminator": [ { "type": "value", "path": "url" } ], "ordered": false, "rules": "open" } }, { "id": "DocumentReference.extension:genomeAssembly", "path": "DocumentReference.extension", "sliceName": "genomeAssembly", "sliceIsConstraining": false, "label": "genomeAssembly", "short": "The genome assembly the contents of this file was called against.", "definition": "The genome assembly the contents of this file was called against. We recommend using the Genome Reference Consortium nomenclature e.g. GRCh37, GRCh38.", "min": 1, "max": "1", "type": [ { "code": "Extension", "profile": [ "http://ga4gh.org/fhir/phenopackets/StructureDefinition/htsfile-genome-assembly" ] } ], "mustSupport": true, "isModifier": false }, { "id": "DocumentReference.status", "path": "DocumentReference.status", "fixedCode": "current", "mustSupport": true }, { "id": "DocumentReference.type", "path": "DocumentReference.type", "label": "htsFormat", "requirements": "The high throughput sequencing file formats are not available in LOINC.", "min": 1, "mustSupport": true, "binding": { "strength": "required", "description": "This indicates which format the file has.", "valueSet": "http://ga4gh.org/fhir/phenopackets/ValueSet/hts-format" } }, { "id": "DocumentReference.subject", "path": "DocumentReference.subject", "type": [ { "code": "Reference", "targetProfile": [ "http://ga4gh.org/fhir/phenopackets/StructureDefinition/Phenopacket", "http://ga4gh.org/fhir/phenopackets/StructureDefinition/Cohort", "http://ga4gh.org/fhir/phenopackets/StructureDefinition/Family" ] } ], "mustSupport": true } ] } }