| Package | hl7.fhir.uv.phenomics-exchange |
| Type | ImplementationGuide |
| Id | Id |
| FHIR Version | R4 |
| Source | http://hl7.org/fhir/uv/phenomics-exchange/https://build.fhir.org/ig/HL7/phenomics-exchange-ig/index.html |
| Url | http://hl7.org/fhir/uv/phenomics-exchange/ImplementationGuide/hl7.fhir.uv.phenomics-exchange |
| Version | 0.1.0 |
| Status | draft |
| Date | 2024-06-18T22:11:07+00:00 |
| Name | PhenomicsExchange |
| Title | Phenomics Exchange for Research and Diagnostics |
| Experimental | False |
| Realm | uv |
| Authority | hl7 |
| Description | FHIR implementation guide for the Global Alliance for Genomics and Health Phenopacket standard. |
| Copyright | [Global Alliance for Genomics and Health](https://www.ga4gh.org) |
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Note: links and images are rebased to the (stated) source
The official URL for this implementation guide is:
http://hl7.org/fhir/uv/phenomics-exchange/ImplementationGuide/hl7.fhir.uv.phenomics-exchange
FHIR implementation guide for the Global Alliance for Genomics and Health Phenopacket standard.
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},
"name" : "CHF-stageIII",
"description" : "Congestive heart failure, New York Heart Association stage III",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/CHF-with-severity"
},
"name" : "CHF-with-severity",
"description" : "PhenotypicFeature Example for severe Low-output congestive heart failure",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/CodedOnset"
},
"name" : "Coded Onset",
"description" : "The onset of a disease using an ontology class.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/DiagnosticMarker"
},
"name" : "Diagnostic Marker",
"description" : "Clinically relevant biomarkers. Most of the assays such as immunohistochemistry (IHC) are covered by the NCIT under the sub-hierarchy NCIT:C36292 (Laboratory Test Result), e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/DiagnosticMarker"
},
"name" : "Diagnostic Marker",
"description" : "Codes to indicate clinically relevant bio markers.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/Disease"
},
"name" : "Disease profile",
"description" : "This profile stipulates that a FHIR Condition must have a codeable concept that represents the disease. The concepts can be taken from various ontologies, but for rare-disease concepts, we recommend MONDO.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/example-patient"
},
"name" : "example-patient",
"description" : "Example of Patient",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Individual"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Condition"
}
],
"reference" : {
"reference" : "Condition/excluded-disease"
},
"name" : "excluded-disease",
"description" : "Phenopacket Example for an excluded disease",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/hp.0003557"
},
"name" : "fiberSizeVariability",
"description" : "Increased variability in muscle fiber diameter (HP:0003557)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/filter-status"
},
"name" : "Filter Status",
"description" : "Filter status: PASS if this position has passed all filters.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/geno-ontology-allelic-state-vs"
},
"name" : "GENO Ontology Allelic State Value Set",
"description" : "Descendent terms of GENO_0000875",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/globalDevelopmentalDelay"
},
"name" : "globalDevelopmentalDelay",
"description" : "Global developmental delay (HP:0001263)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/HistologicalDiagnosis"
},
"name" : "Histological Diagnosis",
"description" : "This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis (which could be reported in the Phenopacket that contains this Biosample). Normal samples would be tagged with the term “NCIT:C38757â€, “Negative Findingâ€.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/HistologicalDiagnosis"
},
"name" : "HistologicalDiagnosis",
"description" : "Histological diagnosis codes from NCIT.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/HpoSeverity"
},
"name" : "Hpo Severity Value Set",
"description" : "The HPO codes for phenotypic feature severity",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/HtsFormat"
},
"name" : "HTS Format",
"description" : "An enumeration used to represent different high-throughput sequencing file formats.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/hypotonia"
},
"name" : "hypotonia",
"description" : "Hypotonia (HP:0001252)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/Individual"
},
"name" : "Individual",
"description" : "The subject of the Phenopacket is represented by an Individual element. This element intends to represent an individual human or other organism.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Condition"
}
],
"reference" : {
"reference" : "Condition/intellectualDisabilityDisease"
},
"name" : "intellectualDisabilityDisease",
"description" : "Intellectual disability (disease)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/interpretation-status"
},
"name" : "Interpretation Status",
"description" : "Describes the conclusion made about the genomic interpretation.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/interpretationStatus-vs"
},
"name" : "Interpretation Status Value Set",
"description" : "Describes the conclusion made about the genomic interpretation.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/KaryotypicSex"
},
"name" : "Karyotypic Sex",
"description" : "Karyotypic sex of an individual (also known as chromosomal sex).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/KaryotypicSex"
},
"name" : "Karyotypic sex code system",
"description" : "karyotypic sex of an individual (also known as chromosomal sex)",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/KaryotypicSex"
},
"name" : "Karyotypic sex value set",
"description" : "The karyotypic (chromosomal) sex of an individual",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/longPhiltrum"
},
"name" : "longPhiltrum",
"description" : "Long philtrum (HP:0000343)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "MedicationAdministration"
}
],
"reference" : {
"reference" : "MedicationAdministration/losartan"
},
"name" : "losartan",
"description" : "Treatment Example (Losartan))",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Treatment"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/lowSetEars"
},
"name" : "lowSetEars",
"description" : "Low-set ears (HP:0000369)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/lvdysfunction-excluded"
},
"name" : "lvdysfunction-excluded",
"description" : "PhenotypicFeature Example for exclusion of LV dysfunction",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/MaterialSample"
},
"name" : "Material Sample",
"description" : "Type of sample (diseases, control, etc.)",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/Measurement"
},
"name" : "Measurement",
"description" : "This profile defines the GA4GH Measurement element in terms of the FHIR Observation",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/MeasurementExt"
},
"name" : "Measurement (Biosample)",
"description" : "Term representing a measurement made on a Biosample",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/microphthalmia"
},
"name" : "microphthalmia",
"description" : "Long philtrum (HP:0000568)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/molecule-context"
},
"name" : "Molecule Context",
"description" : "The molecular context of the vrs variation.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/moleculeContext-vs"
},
"name" : "Molecule Context Value Set",
"description" : "Describes The molecular context of the variant. Default is unspecified_molecule_context.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Specimen"
}
],
"reference" : {
"reference" : "Specimen/biosample.specimen.id.2"
},
"name" : "muscleBiopsy",
"description" : "Biosample Example -- muscle biopsy",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Biosample"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/muscleWeakness"
},
"name" : "muscleWeakness",
"description" : "Muscle weakness (HP:0001324)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/MVP-with-onset"
},
"name" : "MVP-with-onset",
"description" : "PhenotypicFeature Example for mitral value prolapse with onset",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/observation-categories"
},
"name" : "Observation categories",
"description" : "ValueSet description here",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/phenotypicFeatureVS"
},
"name" : "Observation Codes for status of a PhenotypicFeature",
"description" : "The LOINC codes for present if a feature is observed and absent if a feature was excluded.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/Onset"
},
"name" : "Onset",
"description" : "Describes the age at which a phenotypic feature was first noticed or diagnosed.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/Onset"
},
"name" : "Onset ValueSet",
"description" : "Set of HPO codes that denote the onset of a disease or phenotypic feature. The codes are descendants of Onset (HP:0003674) or from SNOMED_CT (282032007).",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/PathologicalTnmFinding"
},
"name" : "Pathological TNM Finding",
"description" : "Pathological TNM findings, if applicable. Corresponds to pathological_tnm_finding (GA4GH)",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/PathologicalStage"
},
"name" : "Pathological Tumor Stage",
"description" : "This element can be used if the phenopacket describes cancer. Tumor staging describes the extent of growth of cancer, including the tumor and, if applicable, affected lymph nodes and distant metastases. This element should not be confused with clinical stage.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/PeterGeneticist"
},
"name" : "PeterGeneticist",
"description" : "Extended example: example practitioner",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Composition"
}
],
"reference" : {
"reference" : "Composition/DevelopmentalDelay"
},
"name" : "Phenopacket (static snapshot of clinical findings to support differential diagnosis of a child with developmental delay).",
"description" : "Example use case for a child with undiagnosed developmental delay",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Phenopacket"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/phenopacketPatientExample01"
},
"name" : "phenopacket Patient Example01",
"description" : "This is an example of a patient resource to be used in the assocaited patient examples. It is not representative of phenopackets patient's data representation",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Practitioner"
}
],
"reference" : {
"reference" : "Practitioner/PhenopacketPractitionerExample01"
},
"name" : "phenopacket Practitioner Example01",
"description" : "This is an incomplete example that used as \n a placeholder for a curated Practitioner example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/Phenopacket"
},
"name" : "Phenopacket profile",
"description" : "This is the main element that represents the Phenopacket in FHIR.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Specimen"
}
],
"reference" : {
"reference" : "Specimen/phenopacketSpecimenExample01"
},
"name" : "phenopacket Specimen Example01",
"description" : "This is an incomplete example that used as\n a placeholder for a curated specimen example",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/phenopackets-genomic-interpretation"
},
"name" : "Phenopackets Genomic Interpretation",
"description" : "A profile of Genomics Reporting Genomics Report profile that represents relevant \n phenopackets building blocks.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/PhenopacketsGenomicInterpretationExample01"
},
"name" : "Phenopackets Genomic Interpretation Example-1",
"description" : "This is an example of phenopackets-variant which is a phenopackets profile of\n the genomics reporting Genomics Report profile.\n It represents phenopackets GenomicInterpretation building block, i.e., the\n interpretation for an individual variant or gene.",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "DiagnosticReport"
}
],
"reference" : {
"reference" : "DiagnosticReport/PhenopacketsGenomicInterpretationExample02"
},
"name" : "Phenopackets Genomic Interpretation Example-2",
"description" : "This is an example of phenopackets-variant which is a phenopackets profile of\n the genomics reporting Genomics Report profile.\n It represents phenopackets GenomicInterpretation building block, i.e., the\n interpretation for an individual variant or gene.",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/phenopackets-variant"
},
"name" : "Phenopackets Variant",
"description" : "A profile of Genomics Reporting Variant profile that represents relevant phenopackets building blocks.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/PhenopacketsVariantExample01"
},
"name" : "Phenopackets Variant Example-1",
"description" : "This is an example of phenopackets-genomic-interpretation\n which is a phenopackets profile of the genomics reporting Variant profile.\n It represents phenopackets GeneDescriptor, VariationDescriptor, VcfRecord,\n and VariantInterpretation building blocks.",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-variant"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Bundle"
}
],
"reference" : {
"reference" : "Bundle/PhenopacketsBundleExample01"
},
"name" : "PhenopacketsBundleExample01",
"description" : "Example Phenopacket Bundle instance",
"exampleBoolean" : true
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/phenotypic-abnormality"
},
"name" : "Phenotypic abnormality ValueSet",
"description" : "ValueSet description here",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/phenotypic-component"
},
"name" : "Phenotypic component ValueSet",
"description" : "ValueSet description here",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/PhenotypicFeature"
},
"name" : "Phenotypic Feature",
"description" : "This profile defines the GA4GH PhenotypicFeature element in terms of the FHIR Observation",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/PhenotypicFeatureExt"
},
"name" : "Phenotypic Feature (Biosample)",
"description" : "Term representing phenotypic features of a Biosample",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/PhenotypicModifierValueSet"
},
"name" : "Phenotypic modifier ValueSet",
"description" : "Human Phenotype Ontology (HPO) Clinical Modifier terms",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/phred-quality-score"
},
"name" : "Phred Quality Score",
"description" : "Used to include Phred-scaled quality score for the assertion made in ALT.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/Polydactyly-with-modifier"
},
"name" : "Polydactyly-with-modifier",
"description" : "Bilateral postaxial Polydactyly, example to demonstrate use of Clinical Modifier",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Patient"
}
],
"reference" : {
"reference" : "Patient/Proband1"
},
"name" : "Proband1",
"description" : "Example child with developmental delay",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Individual"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/reducedVisualAcuity"
},
"name" : "reducedVisualAcuity",
"description" : "Reduced visual acuity (HP:0007663)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/related-concept-id"
},
"name" : "Related Concept ID",
"description" : "Used to provide identifiers to alternative resources representing related, but not equivalent concepts, for example gene ortholog ids",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/retinalDetachment"
},
"name" : "retinalDetachment",
"description" : "Retinal detachment (HP:0000541)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "CodeSystem"
}
],
"reference" : {
"reference" : "CodeSystem/section-type"
},
"name" : "Section Type",
"description" : "Section Type",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/sequence-ontology-structural-variant-vs"
},
"name" : "Sequence Ontology Structural Variant Value Set",
"description" : "Descendent terms of SO:0001537.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "SearchParameter"
}
],
"reference" : {
"reference" : "SearchParameter/service-request-supporting-info"
},
"name" : "service-request-supporting-info",
"description" : "Search ServiceRequest by supporting resource parameters",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/Taxonomy"
},
"name" : "Taxonomy",
"description" : "Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/Taxonomy"
},
"name" : "Taxonomy",
"description" : "Taxonomic identifiers of an organism.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/tga"
},
"name" : "tga",
"description" : "Transposition of the great arteries (HP:0001669)",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/therapeutic-actionability"
},
"name" : "Therapeutic Actionability",
"description" : "one of the five ACMG pathogenicity categories, or NOT_PROVIDED. The default is NOT_PROVIDED.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/therapeuticActionability-vs"
},
"name" : "Therapeutic Actionability Value Set",
"description" : "Describes the therapeutic actionability of the variant.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Composition"
}
],
"reference" : {
"reference" : "Composition/PhenopacketCompositionExample01"
},
"name" : "This is an example of a composition resource that represents some of the Phenopackets data elements",
"description" : "Example Phenopacket Composition instance",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Phenopacket"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Observation"
}
],
"reference" : {
"reference" : "Observation/thrombocytopenia"
},
"name" : "thrombocytopenia",
"description" : "Measurement Example for thrombocytopenia",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Measurement"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:resource"
}
],
"reference" : {
"reference" : "StructureDefinition/Treatment"
},
"name" : "Treatment",
"description" : "This profile defines the GA4GH Treatment element in terms of the FHIR MedicationAdministration",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/TumorGrade"
},
"name" : "Tumor Grade",
"description" : "List of terms representing the tumor grade.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/TumorGrade"
},
"name" : "Tumor Grade",
"description" : "Codes to indicate the grade of a tumor.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/TumorProgression"
},
"name" : "Tumor Progression",
"description" : "This field can be used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence. There are multiple ways of representing this using ontology terms, and the terms chosen should have a specific meaning that is application specific.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/TumorProgression"
},
"name" : "Tumor Progression",
"description" : "Codes to indicate if a specimen is from the primary tumor, a metastasis or a recurrence.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "ValueSet"
}
],
"reference" : {
"reference" : "ValueSet/TumorStage"
},
"name" : "Tumor Stage",
"description" : "Codes to represent the stage of a tumor.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/vcf-info"
},
"name" : "VCF Info",
"description" : "Additional information: Semicolon-separated series of additional information fields from VCF info field.",
"exampleBoolean" : false
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "Condition"
}
],
"reference" : {
"reference" : "Condition/vitreoretinochoroidopathy"
},
"name" : "vitreoretinochoroidopathy",
"description" : "Phenopacket Example for autosomal dominant vitreoretinochoroidopathy",
"exampleCanonical" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/resource-information",
"valueString" : "StructureDefinition:extension"
}
],
"reference" : {
"reference" : "StructureDefinition/vrs-object"
},
"name" : "VRS Object",
"description" : "The VRS Variation object (Link: https://vrs.ga4gh.org/en/stable/)",
"exampleBoolean" : false
}
],
"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",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "ga4gh.html"
}
],
"nameUrl" : "ga4gh.html",
"title" : "GA4GH",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "genomicDiagnostics.html"
}
],
"nameUrl" : "genomicDiagnostics.html",
"title" : "Genomic Diagnostics",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "phenotype.html"
}
],
"nameUrl" : "phenotype.html",
"title" : "Deep phenotyping",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "modeling.html"
}
],
"nameUrl" : "modeling.html",
"title" : "Modeling phenotypic data",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "hpo.html"
}
],
"nameUrl" : "hpo.html",
"title" : "Human Phenotype Ontology",
"generation" : "markdown"
},
{
"extension" : [
{
"url" : "http://hl7.org/fhir/tools/StructureDefinition/ig-page-name",
"valueUrl" : "examples.html"
}
],
"nameUrl" : "examples.html",
"title" : "Examples",
"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.