{ "resourceType": "StructureDefinition", "text": { "status": "generated", "div": "
\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\" Observation 0..*Genomics Base Observation
\".\"\".\"\".\" bodySite 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
\".\"\".\"\".\" observation-secondaryFinding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.\n\nFor more detail, please see:\nhttps://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
\".\"\".\"\".\" basedOn 0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
\".\"\".\"\".\" status 1..1code
\".\"\".\"\".\" category 1..*CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\" coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\" system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
\".\"\".\"\".\"\".\"\".\" code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
\".\"\".\"\".\" code 1..1CodeableConcept
\".\"\".\"\".\" subject 0..1Reference(Patient | Group | Location)
\".\"\".\"\".\" effectiveDateTime 0..1dateTimeClinically relevant time/time-period for observation
\".\"\".\"\".\" issued 0..1instantDate/Time this version was made available
\".\"\".\"\".\" performer 0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
\".\"\".\"\".\" interpretation 0..0
\".\"\".\"\".\" component 0..*BackboneElement
\".\"\".\"\".\"\".\" interpretation 0..0

\"doco\" Documentation for this format
" }, "url": "http://hl7.org/fhir/StructureDefinition/Variant", "version": "1.0.0", "name": "GoshVariant", "title": "Genomics Base Observation", "status": "draft", "experimental": false, "date": "2017-05-20T04:00:00+00:00", "publisher": "HL7 Clinical Genomics WG", "description": "Observation-related profiles", "fhirVersion": "4.0.1", "mapping": [ { "identity": "workflow", "uri": "http://hl7.org/fhir/workflow", "name": "Workflow Pattern" }, { "identity": "sct-concept", "uri": "http://snomed.info/conceptdomain", "name": "SNOMED CT Concept Domain Binding" }, { "identity": "v2", "uri": "http://hl7.org/v2", "name": "HL7 v2 Mapping" }, { "identity": "rim", "uri": "http://hl7.org/v3", "name": "RIM Mapping" }, { "identity": "w5", "uri": "http://hl7.org/fhir/fivews", "name": "FiveWs Pattern Mapping" }, { "identity": "sct-attr", "uri": "http://snomed.org/attributebinding", "name": "SNOMED CT Attribute Binding" } ], "kind": "resource", "abstract": false, "type": "Observation", "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation", "derivation": "constraint", "differential": { "element": [ { "id": "Observation", "path": "Observation", "short": "Genomics Base Observation", "definition": "Base profile that defines characteristics shared by all genetic observations.", "mustSupport": false }, { "id": "Observation.meta", "path": "Observation.meta" }, { "id": "Observation.meta.profile", "path": "Observation.meta.profile", "type": [ { "code": "canonical", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/StructureDefinition", "http://hl7.org/fhir/StructureDefinition/Variant" ] } ] }, { "id": "Observation.extension", "path": "Observation.extension", "slicing": { "discriminator": [ { "type": "value", "path": "url" } ], "rules": "open" } }, { "id": "Observation.extension:BodyStructure", "path": "Observation.extension", "sliceName": "BodyStructure", "definition": "Allows associating observations to a particular portion of the patient - a fetus, a tumor, a lesion, etc.", "type": [ { "code": "Extension", "profile": [ "http://hl7.org/fhir/StructureDefinition/bodySite" ] } ], "mustSupport": false }, { "id": "Observation.extension:SecondaryFinding", "path": "Observation.extension", "sliceName": "SecondaryFinding", "definition": "Allows flagging observations that should be considered secondary findings.", "type": [ { "code": "Extension", "profile": [ "http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding" ] } ], "mustSupport": false }, { "id": "Observation.basedOn", "path": "Observation.basedOn", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/CarePlan", "http://hl7.org/fhir/StructureDefinition/DeviceRequest", "http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation", "http://hl7.org/fhir/StructureDefinition/MedicationRequest", "http://hl7.org/fhir/StructureDefinition/NutritionOrder", "http://hl7.org/fhir/StructureDefinition/ServiceRequest" ] } ], "mustSupport": false }, { "id": "Observation.status", "path": "Observation.status", "comment": "… This should generally be 'completed' or 'revised'.", "mustSupport": false }, { "id": "Observation.category", "path": "Observation.category", "comment": "… This should be populated with 'lab'.", "min": 1, "patternCodeableConcept": { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "Laboratory" } ] }, "mustSupport": false }, { "id": "Observation.code", "path": "Observation.code", "mustSupport": false }, { "id": "Observation.code.coding", "path": "Observation.code.coding", "fixedCoding": { "system": "http://loinc.org", "code": "69548-6", "display": "Genetic variant assessment" } }, { "id": "Observation.code.coding.system", "path": "Observation.code.coding.system", "code": [ { "system": "http://loinc.org", "code": "69548-6", "display": "Genetic variant assessment" } ] }, { "id": "Observation.subject", "path": "Observation.subject", "comment": "… This must be the same patient as on the DiagnosticReport unless combining data from multiple fetuses or family members in a single report.", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Patient", "http://hl7.org/fhir/StructureDefinition/Group", "http://hl7.org/fhir/StructureDefinition/Location" ] } ], "mustSupport": false }, { "id": "Observation.effective[x]", "path": "Observation.effective[x]", "slicing": { "discriminator": [ { "type": "type", "path": "$this" } ] } }, { "id": "Observation.effective[x]:effectiveDateTime", "path": "Observation.effective[x]", "sliceName": "effectiveDateTime", "type": [ { "code": "dateTime" } ], "mustSupport": false }, { "id": "Observation.issued", "path": "Observation.issued", "mustSupport": false }, { "id": "Observation.performer", "path": "Observation.performer", "max": "1", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Practitioner", "http://hl7.org/fhir/StructureDefinition/Organization" ] } ], "mustSupport": false }, { "id": "Observation.interpretation", "path": "Observation.interpretation", "max": "0", "mustSupport": false }, { "id": "Observation.note.author[x]", "path": "Observation.note.author[x]", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Practitioner", "http://hl7.org/fhir/StructureDefinition/Patient", "http://hl7.org/fhir/StructureDefinition/RelatedPerson", "http://hl7.org/fhir/StructureDefinition/Organization" ] }, { "code": "string" } ] }, { "id": "Observation.specimen", "path": "Observation.specimen", "type": [ { "code": "Reference", "targetProfile": [ "http://hl7.org/fhir/StructureDefinition/Specimen" ] } ] }, { "id": "Observation.component", "path": "Observation.component", "label": "variants reference assembly if applicable", "mustSupport": false }, { "id": "Observation.component.code.coding", "path": "Observation.component.code.coding", "code": [ { "system": "http://loinc.org", "code": "62374-4", "display": "Human reference sequence assembly version" }, { "system": "http://loinc.org", "code": "48000-4", "display": "Chromosome [ID]" }, { "system": "http://loinc.org", "code": "48013-7", "display": "Genomic reference sequence [ID]" }, { "system": "http://loinc.org", "code": "69547-8", "display": "Genomic reference allele [ID]" }, { "system": "http://loinc.org", "code": "69551-0", "display": "Genomic alt allele [ID]" }, { "system": "http://loinc.org", "code": "92882-6", "display": "Genomic coordinate system [Type]" }, { "system": "http://loinc.org", "code": "81254-5", "display": "Genomic allele start-end" }, { "system": "http://loinc.org", "code": "48002-0", "display": "Genomic source class [Type]" }, { "system": "http://loinc.org", "code": "53034-5", "display": "Allelic state" }, { "system": "http://loinc.org", "code": "48018-6", "display": "Gene studied [ID]" }, { "system": "http://loinc.org", "code": "81290-9", "display": "Genomic DNA change (gHGVS)" }, { "system": "http://loinc.org", "code": "51958-7", "display": "Transcript reference sequence [ID]" }, { "system": "http://loinc.org", "code": "48004-6", "display": "DNA change (c.DNA)" }, { "system": "http://loinc.org", "code": "48019-4", "display": "DNA change type" }, { "system": "http://loinc.org", "code": "81255-2", "display": "dbSNP [ID]" }, { "system": "http://loinc.org", "code": "79742-3", "display": "Inheritance pattern based on family history" }, { "system": "http://loinc.org", "code": "48005-3", "display": "Amino acid change (pHGVS)" }, { "system": "http://loinc.org", "code": "48006-1", "display": "Amino acid chnage [Type]" } ], "min": 1 }, { "id": "Observation.component.interpretation", "path": "Observation.component.interpretation", "max": "0", "mustSupport": false } ] } }