| Package | hl7.fhir.uv.genomics-reporting |
| Type | ImplementationGuide |
| Id | Id |
| FHIR Version | R4 |
| Source | http://hl7.org/fhir/uv/genomics-reporting/https://build.fhir.org/ig/HL7/genomics-reporting/index.html |
| Url | http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/hl7.fhir.uv.genomics-reporting |
| Version | 3.0.0 |
| Status | active |
| Date | 2024-12-12T20:13:16+00:00 |
| Name | GenomicsReporting |
| Title | Genomics Reporting Implementation Guide |
| Experimental | False |
| Realm | uv |
| Authority | hl7 |
| Description | Guidelines for reporting of clinical genomics results using HL7 FHIR. |
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Note: links and images are rebased to the (stated) source
Generated Narrative: ImplementationGuide hl7.fhir.uv.genomics-reporting
The official URL for this implementation guide is:
http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/hl7.fhir.uv.genomics-reporting
Guidelines for reporting of clinical genomics results using HL7 FHIR.
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],
"reference" : {
"reference" : "Bundle/bundle-cgexample"
},
"name" : "bundle-cgexample",
"description" : "Example bundle showing a variety of profiles.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-cgexample-withGrouping"
},
"name" : "bundle-cgexample-withGrouping",
"description" : "Example bundle showing a variety of profiles, including how groupings of Observations might be delivered.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-complexVariant-nonHGVS"
},
"name" : "bundle-complexVariant-nonHGVS",
"description" : "Example bundle with compound heterozygous variant, where the specific changes are represented without HGVS.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-compound-heterozygote"
},
"name" : "bundle-compound-heterozygote",
"description" : "Example bundle with compound heterozygous variant, where the specific changes are represented with HGVS.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-CYP2C19"
},
"name" : "bundle-CYP2C19",
"description" : "Example bundle containing CYP2C19 report and variants",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-oncology-diagnostic"
},
"name" : "bundle-oncology-diagnostic",
"description" : "Example of an oncology report, TMB, variants, and implications.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-oncology-report-example"
},
"name" : "bundle-oncology-report-example",
"description" : "Example oncology bundle including report, variants, and other resources.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-oncologyexamples-r4"
},
"name" : "bundle-oncologyexamples-r4",
"description" : "Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-oncologyexamples-r4-withGrouping"
},
"name" : "bundle-oncologyexamples-r4-withGrouping",
"description" : "Example bundle with an oncology report with SNVs, TMB, MSI, and therapy matches, including some groupings of observations",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-pgxexample"
},
"name" : "bundle-pgxexample",
"description" : "Example bundle with a PGx report and a variety of observations.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/bundle-sequence-phase-relation-CYP2C19"
},
"name" : "bundle-sequence-phase-relation-CYP2C19",
"description" : "Example Sequence Phase Relation showing a report with two variants in cis",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/CGPatientExample01"
},
"name" : "CGPatientExample01",
"description" : "Example for Patient. Supports references to subject for multiple genomics reporting profile conforming instances.",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/clinvar-evidence-level-custom-cs"
},
"name" : "ClinVar Evidence Level Example Codes",
"description" : "ClinVar contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on ClinVar https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/ . These examples are informational only, for copyright information contact the relevant source.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/CNVAnalysis-called"
},
"name" : "CNVAnalysis-called",
"description" : "CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:complex-type"
}
],
"reference" : {
"reference" : "StructureDefinition/coded-annotation"
},
"name" : "Coded Annotation",
"description" : "Annotation DataType with added CodeableConcept extension element",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/coded-annotation-types-cs"
},
"name" : "Coded Annotation Type Codes",
"description" : "Code System for specific types of coded annotations",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/coded-annotation-types-vs"
},
"name" : "Coded Annotation Types",
"description" : "Value Set for specific types of coded annotations",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/condition-inheritance-mode-vs"
},
"name" : "Condition Inheritance Patterns",
"description" : "Value Set for specific transmission patterns of a condition in a pedigree",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/denovoChild"
},
"name" : "denovoChild",
"description" : "Child of a trio",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/denovoFather"
},
"name" : "denovoFather",
"description" : "Father of a trio",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/denovoMother"
},
"name" : "denovoMother",
"description" : "Mother of a trio",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/diagnostic-implication"
},
"name" : "Diagnostic Implication",
"description" : "Observation stating a diagnostic annotation (e.g. disease risk) on one or more genotype/haplotype/variant/biomarker observations.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/diagnosticImplication-interact-smn1-smn2"
},
"name" : "diagnosticImplication-interact-smn1-smn2",
"description" : "Diagnostic Implication for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/diagnosticreport-hla-glstring-r4"
},
"name" : "diagnosticreport-hla-glstring-r4",
"description" : "Example GenomicReport including an HLA glstring",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/dna-change-type-vs"
},
"name" : "DNA Change Type",
"description" : "DNA Change Type of a variant.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ConceptMap"
}
],
"reference" : {
"reference" : "ConceptMap/dna-change-type-map"
},
"name" : "DNA Change Type Map",
"description" : "Mapping from http://loinc.org ValueSet for DNA Change Type to http://www.sequenceontology.org codes",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/EGFR-L858R-molc"
},
"name" : "EGFR-L858R-molc",
"description" : "Example Molecular Consequence EGFR L858R missense_variant",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/EGFR-L858R-significance"
},
"name" : "EGFR-L858R-significance",
"description" : "Example DiagnosticImplication - EGFR pathogenic",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/EGFR-L858R-therapuDrug1"
},
"name" : "EGFR-L858R-therapuDrug1",
"description" : "Example of EGFR-L858R Therapeutic Implication for drug treatment 1",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/EGFR-L858R-therapuDrug2"
},
"name" : "EGFR-L858R-therapuDrug2",
"description" : "Example of EGFR-L858R Therapeutic Implication for drug treatment 2",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/EGFR-L858R-var"
},
"name" : "EGFR-L858R-var",
"description" : "Example for EGFR L858R",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ServiceRequest"
}
],
"reference" : {
"reference" : "ServiceRequest/eMERGEServiceRequest"
},
"name" : "eMERGEServiceRequest",
"description" : "Example PGx Service Request",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/evidence-level-example-vs"
},
"name" : "Evidence Level Examples",
"description" : "Example sources of values for Evidence Level",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleGermlineCNV"
},
"name" : "ExampleGermlineCNV",
"description" : "Example for germline CNV",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleGermlineDEL"
},
"name" : "ExampleGermlineDEL",
"description" : "Example for germline DEL",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleGermlineINV"
},
"name" : "ExampleGermlineINV",
"description" : "Example for germline INV",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Organization"
}
],
"reference" : {
"reference" : "Organization/ExampleLab"
},
"name" : "ExampleLab",
"description" : "Organization (lab) example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Organization"
}
],
"reference" : {
"reference" : "Organization/ExampleOrg"
},
"name" : "ExampleOrg",
"description" : "Example Org",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/ExamplePatient"
},
"name" : "ExamplePatient",
"description" : "Patient example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ServiceRequest"
}
],
"reference" : {
"reference" : "ServiceRequest/ExampleServiceRequest"
},
"name" : "ExampleServiceRequest",
"description" : "ServiceRequest (order) example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleSomaticCNV"
},
"name" : "ExampleSomaticCNV",
"description" : "Example for somatic CNV",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleSomaticDEL"
},
"name" : "ExampleSomaticDEL",
"description" : "Example for somatic DEL",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ExampleSomaticINV"
},
"name" : "ExampleSomaticINV",
"description" : "Example for somatic INV",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Specimen"
}
],
"reference" : {
"reference" : "Specimen/ExampleSpecimen"
},
"name" : "ExampleSpecimen",
"description" : "Specimen example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-dx-implications"
},
"name" : "Find Population Diagnostic Implications",
"description" : "Retrieve count or list of patients having diagnostic implications.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-molecular-consequences"
},
"name" : "Find Population Molecular Consequences",
"description" : "Retrieve count or list of patients having molecular consequences.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-specific-haplotypes"
},
"name" : "Find Population Specific Haplotypes",
"description" : "Retrieve count or list of patients having specified genotypes/haplotypes.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-specific-variants"
},
"name" : "Find Population Specific Variants",
"description" : "Retrieve count or list of patients having specified variants.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-structural-intersecting-variants"
},
"name" : "Find Population Structural Intersecting Variants",
"description" : "Retrieve count or list of patients having structural intersecting variants in specified regions.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-structural-subsuming-variants"
},
"name" : "Find Population Structural Subsuming Variants",
"description" : "Retrieve count or list of patients having structural subsuming variants in specified regions.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-population-tx-implications"
},
"name" : "Find Population Treatment Implications",
"description" : "Retrieve count or list of patients having therapeutic implications.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-study-metadata"
},
"name" : "Find Study Metadata",
"description" : "Retrieve metadata about sequencing studies performed on a subject.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-dx-implications"
},
"name" : "Find Subject Diagnostic Implications",
"description" : "Retrieves genetic diagnostic implications for variants.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-haplotypes"
},
"name" : "Find Subject Haplotypes",
"description" : "Retrieve haplotypes/genotypes for specified genes.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-molecular-consequences"
},
"name" : "Find Subject Molecular Consequences",
"description" : "Retrieves molecular consequences of a DNA variant.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-specific-haplotypes"
},
"name" : "Find Subject Specific Haplotypes",
"description" : "See if specified haplotypes/genotypes are present.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-specific-variants"
},
"name" : "Find Subject Specific Variants",
"description" : "Determine if specified simple variants are present.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-structural-intersecting-variants"
},
"name" : "Find Subject Structural Intersecting Variants",
"description" : "Determine if structural variants are present that overlap range(s).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-structural-subsuming-variants"
},
"name" : "Find Subject Structural Subsuming Variants",
"description" : "Determine if structural variants are present that fully subsume a range.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-tx-implications"
},
"name" : "Find Subject Treatment Implications",
"description" : "Retrieves genetic therapeutic implications for variants/haplotypes/genotypes.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "OperationDefinition"
}
],
"reference" : {
"reference" : "OperationDefinition/find-subject-variants"
},
"name" : "Find Subject Variants",
"description" : "Determine if simple variants are present that overlap range(s).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindALLPopulationSpecificVariantsOutput"
},
"name" : "FindALLPopulationSpecificVariantsOutput",
"description" : "Example Output of 'FindPopulationSpecificVariants' Operation, based on 'AND' logic",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindANYPopulationSpecificVariantsOutput"
},
"name" : "FindANYPopulationSpecificVariantsOutput",
"description" : "Example Output of 'FindPopulationSpecificVariants' Operation, based on 'OR' logic",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationDxImplicationsOutput"
},
"name" : "FindPopulationDxImplicationsOutput",
"description" : "Example Output of 'FindPopulationDxImplications' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationMolecConseqOutput"
},
"name" : "FindPopulationMolecConseqOutput",
"description" : "Example Output of 'FindPopulationMolecConseq' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationSpecificHaplotypesOutput"
},
"name" : "FindPopulationSpecificHaplotypesOutput",
"description" : "Example Output of 'FindPopulationSpecificHaplotypes' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationStructuralIntersectingVariantsOutput"
},
"name" : "FindPopulationStructuralIntersectingVariantsOutput",
"description" : "Example Output of 'FindPopulationStructuralIntersectingVariants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationStructuralSubsumingVariantsOutput"
},
"name" : "FindPopulationStructuralSubsumingVariantsOutput",
"description" : "Example Output of 'FindPopulationStructuralSubsumingVariants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindPopulationTxImplicationsOutput"
},
"name" : "FindPopulationTxImplicationsOutput",
"description" : "Example Output of 'FindPopulationTxImplications' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindStudyMetadataOutput"
},
"name" : "FindStudyMetadataOutput",
"description" : "Example Output of 'FindStudyMetadata' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectDxImplicationsOutput"
},
"name" : "FindSubjectDxImplicationsOutput",
"description" : "Example Output of 'FindSubjectDxImplications' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectHaplotypesOutput"
},
"name" : "FindSubjectHaplotypesOutput",
"description" : "Example Output of 'FindSubjectHaplotypes' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectMolecConseqOutput"
},
"name" : "FindSubjectMolecConseqOutput",
"description" : "Example Output of 'FindSubjectMolecConseq' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectSpecificHaplotypesOutput"
},
"name" : "FindSubjectSpecificHaplotypesOutput",
"description" : "Example Output of 'FindSubjectSpecificHaplotypes' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectSpecificVariantsOutput"
},
"name" : "FindSubjectSpecificVariantsOutput",
"description" : "Example Output of 'FindSubjectSpecificVariants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectStructuralIntersectingVariantsOutput"
},
"name" : "FindSubjectStructuralIntersectingVariantsOutput",
"description" : "Example Output of 'FindSubjectStructuralIntersectingVariants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectStructuralSubsumingVariantsOutput"
},
"name" : "FindSubjectStructuralSubsumingVariantsOutput",
"description" : "Example Output of 'FindSubjectStructuralSubsumingVariants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectTxImplicationsOutput"
},
"name" : "FindSubjectTxImplicationsOutput",
"description" : "Example Output of 'FindSubjectTxImplications' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Parameters"
}
],
"reference" : {
"reference" : "Parameters/FindSubjectVariantsOutput"
},
"name" : "FindSubjectVariantsOutput",
"description" : "Example Output of 'Find Subject Variants' Operation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/followup-recommendation"
},
"name" : "Followup Recommendation",
"description" : "Task proposing a follow-up that is recommended based on the implications of genomic findings.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/FullGenome-GRCh38"
},
"name" : "FullGenome-GRCh38",
"description" : "Example for Genomic Data File FullGenome-GRCh38",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/functional-effect-vs"
},
"name" : "Functional Effect Value Set",
"description" : "The effect of a variant on downstream biological products or pathways.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/genetic-therapeutic-implications-vs"
},
"name" : "Genetic Therapeutic Implications",
"description" : "Value Set for terms that describe a predicted ramification based on the presence of associated molecular finding(s).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource:abstract"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-base"
},
"name" : "Genomic Base",
"description" : "Base profile that defines characteristics shared by all genetic observations.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-data-file"
},
"name" : "Genomic Data File",
"description" : "A profile of DocumentReference used to represent a genomics file.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource:abstract"
}
],
"reference" : {
"reference" : "StructureDefinition/finding"
},
"name" : "Genomic Finding",
"description" : "Properties common to genetic findings whose results are expressed as computable discrete elements (e.g. genotypes, haplotypes, variants, etc.).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource:abstract"
}
],
"reference" : {
"reference" : "StructureDefinition/implication"
},
"name" : "Genomic Implication",
"description" : "Properties common to genomic implications expressed as computable discrete elements.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-report"
},
"name" : "Genomic Report",
"description" : "Genomic profile of DiagnosticReport.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-report-note"
},
"name" : "Genomic Report Note",
"description" : "Adds codified notes to a report to capture additional content",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-risk-assessment"
},
"name" : "Genomic Risk Assessment",
"description" : "RiskAssessment delivered as part of a genomics report or observation",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study"
},
"name" : "Genomic Study",
"description" : "A genomic study is a set of analyses performed to analyze and generate genomic data.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis"
},
"name" : "Genomic Study Analysis",
"description" : "A genomic study analysis is a component of a genomic study.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-change-type"
},
"name" : "Genomic Study Analysis Change Type",
"description" : "Defines the types of alterations detectable by a given genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-device"
},
"name" : "Genomic Study Analysis Device",
"description" : "Genomic Study Analysis Device",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-ext"
},
"name" : "Genomic Study Analysis Extension",
"description" : "Used to transmit the one or more analysis per GenomimcStudy",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-focus"
},
"name" : "Genomic Study Analysis Focus",
"description" : "Defines a focus for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-genome-build"
},
"name" : "Genomic Study Analysis Genome Build",
"description" : "Defines the genome build for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-input"
},
"name" : "Genomic Study Analysis Input",
"description" : "Genomic Study Analysis Input",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-method-type"
},
"name" : "Genomic Study Analysis Method Type",
"description" : "Defines a method type for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-metrics"
},
"name" : "Genomic Study Analysis Metrics",
"description" : "Metrics about the sequencing analysis that was performed",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-output"
},
"name" : "Genomic Study Analysis Output",
"description" : "Genomic Study Analysis Output",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-protocol-performed"
},
"name" : "Genomic Study Analysis Protocol Performed",
"description" : "Defines a protocol that was performed for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-regions"
},
"name" : "Genomic Study Analysis Regions",
"description" : "Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-genomic-source-class"
},
"name" : "Genomic Study Analysis Source Class",
"description" : "The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-specimen"
},
"name" : "Genomic Study Analysis Specimen",
"description" : "Defines a specimen for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-analysis-title"
},
"name" : "Genomic Study Analysis Title",
"description" : "Defines a title for a genomic analysis",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/genomic-study-change-type-cs"
},
"name" : "Genomic Study Change Type CodeSystem",
"description" : "Backport of http://hl7.org/fhir/genomicstudy-changetype",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/genomic-study-change-type-vs"
},
"name" : "Genomic Study Change Type ValueSet",
"description" : "Backport of http://hl7.org/fhir/ValueSet/genomicstudy-changetype",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/genomic-study-data-format-cs"
},
"name" : "Genomic Study Data Format CodeSystem",
"description" : "Backport of http://hl7.org/fhir/genomicstudy-dataformat",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/genomic-study-data-format-vs"
},
"name" : "Genomic Study Data Format ValueSet",
"description" : "Backport of http://hl7.org/fhir/ValueSet/genomicstudy-dataformat",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/genomic-study-method-type-cs"
},
"name" : "Genomic Study Method Type CodeSystem",
"description" : "Backport of http://hl7.org/fhir/genomicstudy-methodtype",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/genomic-study-method-type-vs"
},
"name" : "Genomic Study Method Type ValueSet",
"description" : "Backport of http://hl7.org/fhir/ValueSet/genomicstudy-methodtype",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-reference"
},
"name" : "Genomic Study Reference",
"description" : "Used to reference a GenomicStudy profile",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/genomic-study-referrer-ext"
"description" : "Example Molecular Consequence NOTCH1 missense_variant",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/NOTCH1-uncertain-var"
},
"name" : "NOTCH1-uncertain-var",
"description" : "Example for NOTCH1 uncertain",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/NTHL1-snv-disease"
},
"name" : "NTHL1-snv-disease",
"description" : "Example DiagnosticImplication - NTHL1 SNV Hereditary cancer-predisposing syndrome",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/NTHL1-snv-molc"
},
"name" : "NTHL1-snv-molc",
"description" : "Example Molecular Consequence NTHL1 SNV variant with nonsense codon",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/NTHL1-snv-var"
},
"name" : "NTHL1-snv-var",
"description" : "Example for NTHL1 SNV",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/obs-idh-ex"
},
"name" : "obs-idh-ex",
"description" : "Example DiagnosticImplication - Pathogenic for CF",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/obs1-interact-smn1-smn2"
},
"name" : "obs1-interact-smn1-smn2",
"description" : "SMN1 CNV companion for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/obs2-interact-smn1-smn2"
},
"name" : "obs2-interact-smn1-smn2",
"description" : "SMN2 CNV companion for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/orderingPractitioner"
},
"name" : "orderingPractitioner",
"description" : "Example of an ordering provider",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/pathologistPractitioner"
},
"name" : "pathologistPractitioner",
"description" : "Example of a pathologist",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/PDL1Example"
},
"name" : "PDL1Example",
"description" : "Example for PD-L1",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Organization"
}
],
"reference" : {
"reference" : "Organization/performingOrganization"
},
"name" : "performingOrganization",
"description" : "Example of a Pathology lab",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-geno-1001"
},
"name" : "Pgx-geno-1001",
"description" : "Example of a Genotype from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-geno-1002"
},
"name" : "Pgx-geno-1002",
"description" : "Example of a Genotype from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-geno-1003"
},
"name" : "Pgx-geno-1003",
"description" : "Example of a Genotype from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1011"
},
"name" : "Pgx-var-1011",
"description" : "Example variant 1011",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1012"
},
"name" : "Pgx-var-1012",
"description" : "Example variant 1012",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1013"
},
"name" : "Pgx-var-1013",
"description" : "Example variant 1013",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1014"
},
"name" : "Pgx-var-1014",
"description" : "Example variant 1014",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1015"
},
"name" : "Pgx-var-1015",
"description" : "Example variant 1015",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1016"
},
"name" : "Pgx-var-1016",
"description" : "Example variant 1016",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1017"
},
"name" : "Pgx-var-1017",
"description" : "Example variant 1017",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1018"
},
"name" : "Pgx-var-1018",
"description" : "Example variant 1018",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1019"
},
"name" : "Pgx-var-1019",
"description" : "Example variant 1019",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1020"
},
"name" : "Pgx-var-1020",
"description" : "Example variant 1020",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Pgx-var-1021"
},
"name" : "Pgx-var-1021",
"description" : "Example variant 1021",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/PGxGenomicReportEMERGE"
},
"name" : "PGxGenomicReportEMERGE",
"description" : "Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/PGxGenomicReportEMERGE-withGrouping"
},
"name" : "PGxGenomicReportEMERGE-withGrouping",
"description" : "Example of a Report carrying multiple Therapeutic Implications, Genotypes, and Variants",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Procedure"
}
],
"reference" : {
"reference" : "Procedure/PGXGenomicStudy"
},
"name" : "PGXGenomicStudy",
"description" : "Example of PGX sequencing panel",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Procedure"
}
],
"reference" : {
"reference" : "Procedure/PGXGenomicStudyAnalysis"
},
"name" : "PGXGenomicStudyAnalysis",
"description" : "Example of PGX Sequence analysis",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Task"
}
],
"reference" : {
"reference" : "Task/PGxRecEx01"
},
"name" : "PGxRecEx01",
"description" : "Example of a Medication Recommendation for alternatives to clopidogrel",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Task"
}
],
"reference" : {
"reference" : "Task/PGxRecEx02"
},
"name" : "PGxRecEx02",
"description" : "Example of a Medication Recommendation for alternatives to voriconazole",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Task"
}
],
"reference" : {
"reference" : "Task/PGxRecEx03"
},
"name" : "PGxRecEx03",
"description" : "Example of a Medication Recommendation for decreasing dosage for citalopram",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Task"
}
],
"reference" : {
"reference" : "Task/PGxRecEx04"
},
"name" : "PGxRecEx04",
"description" : "Example of a Medication Recommendation for decreasing dosage for escitalopram",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Task"
}
],
"reference" : {
"reference" : "Task/PGxRecEx05"
},
"name" : "PGxRecEx05",
"description" : "Example of a Medication Recommendation for decreasing dosage for amitriptyline",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/pharmgkb-evidence-level-custom-cs"
},
"name" : "PharmGKB Evidence Level Example Codes",
"description" : "PharmGKB contains examples of evidence level concepts that are not conflated with clinical significance. These can be found on PharmGKB https://www.pharmgkb.org/page/clinAnnLevels. These examples are informational only, for copyright information contact the relevant source.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/PolyGenicDiagnosticImpExample"
},
"name" : "PolyGenicDiagnosticImpExample",
"description" : "Example of a Diagnostic Implication for Diabetes Type 2 with a polygenic risk score.",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/practitioner02"
},
"name" : "practitioner02",
"description" : "Example practitioner",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/recommended-action"
},
"name" : "Recommended Action",
"description" : "References a proposed action that is recommended based on the results of the diagnostic report.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/workflow-relatedArtifactComponent"
},
"name" : "Related Artifact for Observation component",
"description" : "Use the RelatedArtifact at the Observation.component element (not valid in the R4 extension)",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/repeat-motif-order"
},
"name" : "Repeat Motif Order",
"description" : "Use to group and order repeat expansion motifs.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/RepeatExpansion"
},
"name" : "RepeatExpansion",
"description" : "Repeat Expansion Variant",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ROS1-Fusion"
},
"name" : "ROS1-Fusion",
"description" : "Example Molecular Consequence ROS1 Fusion",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ROS1-Fusion-disease"
},
"name" : "ROS1-Fusion-disease",
"description" : "Example DiagnosticImplication - ROS1 disease",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ROS1-Fusion-therapuDrug"
},
"name" : "ROS1-Fusion-therapuDrug",
"description" : "Example of ROS1 Fusion Therapeutic Implication for drug treatment",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ROS1-Fusion-therapuTrial"
},
"name" : "ROS1-Fusion-therapuTrial",
"description" : "Example of ROS1 Fusion Therapeutic Implication for Clinical Trial",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ROS1-Fusion-var"
},
"name" : "ROS1-Fusion-var",
"description" : "Example for ROS1 Fusion but as typically reported in PDF, without necessarily declaring a particular fusion partner",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/sequence-phase-relationship"
},
"name" : "Sequence Phase Relationship",
"description" : "Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/sequence-phase-relationship-cs"
},
"name" : "Sequence Phase Relationship Codes",
"description" : "Code System for specific types of relationships",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/sequence-phase-relationship-vs"
},
"name" : "Sequence Phase Relationships",
"description" : "Value Set for specific types of relationships",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/SequencePhaseRelationExample1"
},
"name" : "SequencePhaseRelationExample1",
"description" : "Example for sequence phase relation.",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Procedure"
}
],
"reference" : {
"reference" : "Procedure/SequencingProcedure"
},
"name" : "SequencingProcedure",
"description" : "Very simple producure representing a genomic study's protocol",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ServiceRequest"
}
],
"reference" : {
"reference" : "ServiceRequest/servicerequest-hla-a-r4"
},
"name" : "servicerequest-hla-a-r4",
"description" : "Example ServiceRequest for genomics",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/SimpleVariantAnalysis-called"
},
"name" : "SimpleVariantAnalysis-called",
"description" : "SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/SNVexample"
},
"name" : "SNVexample",
"description" : "Example Variant",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/somaticPatient"
},
"name" : "somaticPatient",
"description" : "Somatic example Patient",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/somaticReport"
},
"name" : "somaticReport",
"description" : "Example somatic GenomicReport",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ServiceRequest"
}
],
"reference" : {
"reference" : "ServiceRequest/somaticServiceRequest"
},
"name" : "somaticServiceRequest",
"description" : "Example for Somatic Testing Request",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Procedure"
}
],
"reference" : {
"reference" : "Procedure/somaticStudy"
},
"name" : "somaticStudy",
"description" : "Example for somatic genetic study",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/somaticVCFfile"
},
"name" : "somaticVCFfile",
"description" : "Example for Genomic Data File somaticVCFfile",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Specimen"
}
],
"reference" : {
"reference" : "Specimen/specimen-hla-r4"
},
"name" : "specimen-hla-r4",
"description" : "Example HLA specimen",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/STAG2-insertion-molc"
},
"name" : "STAG2-insertion-molc",
"description" : "Example Molecular Consequence STAG2 frameshift",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/STAG2-insertion-significance"
},
"name" : "STAG2-insertion-significance",
"description" : "Example DiagnosticImplication - STAG2 likely pathogenic",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/STAG2-insertion-var"
},
"name" : "STAG2-insertion-var",
"description" : "Example for STAG2 insertion",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/supervisorPractitioner"
},
"name" : "supervisorPractitioner",
"description" : "Example of a supervisor",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/therapeutic-implication"
},
"name" : "Therapeutic Implication",
"description" : "Observation stating a therapeutic annotation (e.g. drug susceptibility, clinical trial eligibility) on one or more genotype/haplotype/variant/biomarker observations.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Therapeutic-Implication-Clinical-Trial-2"
},
"name" : "Therapeutic-Implication-Clinical-Trial-2",
"description" : "Example of a Therapeutic Implication for Carbamazepine",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Therapeutic-Implication-Clinical-Trial-Somatic"
},
"name" : "Therapeutic-Implication-Clinical-Trial-Somatic",
"description" : "Example of a Therapeutic Implication for Clinical Trial",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TherapeuticImplicationExample1"
},
"name" : "TherapeuticImplicationExample1",
"description" : "Example of a Therapeutic Implication for Carbamazepine",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/therapuDrug1-interact-smn1-smn2"
},
"name" : "therapuDrug1-interact-smn1-smn2",
"description" : "Antisense Oligonucelotide example of Therapeutic Implication for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/therapuDrug2-interact-smn1-smn2"
},
"name" : "therapuDrug2-interact-smn1-smn2",
"description" : "Transgene example of Therapeutic Implication for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/therapuDrug3-interact-smn1-smn2"
},
"name" : "therapuDrug3-interact-smn1-smn2",
"description" : "Small molecule example of Therapeutic Implication for SMN1/SMN2 CNV example",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/therapy-assessed-reference"
},
"name" : "Therapy Assessed reference to a FHIR resource",
"description" : "Used to reference a specific therapy that was assessed (e.g. a FHIR ResearchStudy, a FHIR CarePlan, or a FHIR PlanDefinition).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TMB-therapuDrug"
},
"name" : "TMB-therapuDrug",
"description" : "Example of high TMB Therapeutic Implication for drug treatment",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TMBExample"
},
"name" : "TMBExample",
"description" : "Example for Tumor Mutation Burden",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/tbd-codes-cs"
},
"name" : "To Be Determined Codes",
"description" : "These codes are 'TBD' codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/tbd-codes-vs"
},
"name" : "To Be Determined Value Set",
"description" : "Value Set for codes yet to be defined in LOINC",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Device"
}
],
"reference" : {
"reference" : "Device/triodenovo-software"
},
"name" : "triodenovo-software",
"description" : "Triodenovo Software",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TumorMutationBurdenExample01"
},
"name" : "TumorMutationBurdenExample01",
"description" : "Example for Tumor Mutation Burden",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Specimen"
}
],
"reference" : {
"reference" : "Specimen/tumorSpecimen"
},
"name" : "tumorSpecimen",
"description" : "Example for tumor specimen",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp01"
},
"name" : "TxImp01",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp02"
},
"name" : "TxImp02",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp03"
},
"name" : "TxImp03",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp04"
},
"name" : "TxImp04",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp05"
},
"name" : "TxImp05",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/TxImp06"
},
"name" : "TxImp06",
"description" : "Example of a Therapeutic Implication from eMERGE",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/UncallableRegions"
},
"name" : "UncallableRegions",
"description" : "Representing a BED file that represents uncallable regions",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/variant"
},
"name" : "Variant",
"description" : "Details about a set of changes in the tested sample compared to a reference sequence.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/variant-confidence-status-vs"
},
"name" : "Variant Confidence Status",
"description" : "A code that classifies the confidence for calling this variant.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/variant-confidence-status-cs"
},
"name" : "Variant Confidence Status Codes",
"description" : "A code that represents the confidence of a true positive variant call.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Variant-Somatic-Clinical-Trial"
},
"name" : "Variant-Somatic-Clinical-Trial",
"description" : "Example for Somatic Variant and Clinical Trial",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/variant-with-molec-consequences"
},
"name" : "variant-with-molec-consequences",
"description" : "Variant with molecular consequences",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/VariantExample"
},
"name" : "VariantExample",
"description" : "Example for Variant NM_004448.4(ERBB2):c.2264_2278del",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/VariantExample1"
},
"name" : "VariantExample1",
"description" : "Example for Variant given by HGVS",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/VariantExample2"
},
"name" : "VariantExample2",
"description" : "Example for genomic Variant given by VCF columns",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/WES-FullSequencedRegion-GRCh38"
},
"name" : "WES-FullSequencedRegion-GRCh38",
"description" : "WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DocumentReference"
}
],
"reference" : {
"reference" : "DocumentReference/WES-UncallableRegions-GRCh38"
},
"name" : "WES-UncallableRegions-GRCh38",
"description" : "Example for Genomic Data File WES-UncallableRegions-GRCh38",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ZFHX3-significance"
},
"name" : "ZFHX3-significance",
"description" : "Example DiagnosticImplication - ZFHX3 uncertain significance",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ZFHX3-uncertain-molc"
},
"name" : "ZFHX3-uncertain-molc",
"description" : "Example Molecular Consequence ZFHX3 missense_variant",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/ZFHX3-uncertain-var"
},
"name" : "ZFHX3-uncertain-var",
"description" : "Example for ZFHX3 uncertain",
"exampleCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
}
],
"page" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "toc.html"
}
],
"nameUrl" : "toc.html",
"title" : "Table of Contents",
"generation" : "html",
"page" : [
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "index.html"
}
],
"nameUrl" : "index.html",
"title" : "Home Page",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "background.html"
}
],
"nameUrl" : "background.html",
"title" : "Genomic Background",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "general.html"
}
],
"nameUrl" : "general.html",
"title" : "General Genomic Reporting",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "sequencing.html"
}
],
"nameUrl" : "sequencing.html",
"title" : "Variant Reporting",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "pharmacogenomics.html"
}
],
"nameUrl" : "pharmacogenomics.html",
"title" : "Pharmacogenomic Reporting",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "somatics.html"
}
],
"nameUrl" : "somatics.html",
"title" : "Somatic Reporting",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "histocompatibility.html"
}
],
"nameUrl" : "histocompatibility.html",
"title" : "Histocompatibility and Immunogenetic Reporting",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "operations.html"
}
],
"nameUrl" : "operations.html",
"title" : "Genomic Operations",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "downloads.html"
}
],
"nameUrl" : "downloads.html",
"title" : "Useful Downloads",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "v2.html"
}
],
"nameUrl" : "v2.html",
"title" : "Appendix A: Relation to v2 reporting",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "cgapps.html"
}
],
"nameUrl" : "cgapps.html",
"title" : "Appendix B: Clinical Genomic Apps",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "domain.html"
}
],
"nameUrl" : "domain.html",
"title" : "Appendix C: HL7 Domain Analysis Model",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "usecases.html"
}
],
"nameUrl" : "usecases.html",
"title" : "Appendix D: Query Guidance",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "codings.html"
}
],
"nameUrl" : "codings.html",
"title" : "Appendix E: External Coding Systems",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "conversion.html"
}
],
"nameUrl" : "conversion.html",
"title" : "Appendix F: Conversion from FHIR Core STU3",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "molecularSequence.html"
}
],
"nameUrl" : "molecularSequence.html",
"title" : "Appendix G: Molecular Sequence",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "groupingGuidance.html"
}
],
"nameUrl" : "groupingGuidance.html",
"title" : "Appendix H: Grouping Guidance",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "Glossary.html"
}
],
"nameUrl" : "Glossary.html",
"title" : "Appendix I: Glossary",
"generation" : "html"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "changes.html"
}
],
"nameUrl" : "changes.html",
"title" : "Change Log",
"generation" : "markdown"
}
]
},
"parameter" : [
{
"code" : "path-resource",
"value" : "input/capabilities"
},
{
"code" : "path-resource",
"value" : "input/examples"
},
{
"code" : "path-resource",
"value" : "input/extensions"
},
{
"code" : "path-resource",
"value" : "input/models"
},
{
"code" : "path-resource",
"value" : "input/operations"
},
{
"code" : "path-resource",
"value" : "input/profiles"
},
{
"code" : "path-resource",
"value" : "input/resources"
},
{
"code" : "path-resource",
"value" : "input/vocabulary"
},
{
"code" : "path-resource",
"value" : "input/maps"
},
{
"code" : "path-resource",
"value" : "input/testing"
},
{
"code" : "path-resource",
"value" : "input/history"
},
{
"code" : "path-resource",
"value" : "fsh-generated/resources"
},
{
"code" : "path-pages",
"value" : "template/config"
},
{
"code" : "path-pages",
"value" : "input/images"
},
{
"code" : "path-tx-cache",
"value" : "input-cache/txcache"
}
]
}
}
XIG built as of ??metadata-date??. Found ??metadata-resources?? resources in ??metadata-packages?? packages.