{ "resourceType": "StructureDefinition", "id": "region-studied", "meta": { "lastUpdated": "2019-12-20T21:26:15.663+00:00" }, "text": { "status": "generated", "div": "
NameFlagsCard.TypeDescription & Constraints\"doco\"
\".\"\".\"Observation0..*Region Studied
\".\"\".\"\".\"code1..1CodeableConceptRegion Studied
Required Pattern: At least the following
\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 53041-0
\".\"\".\"\".\"valueCodeableConcept0..0
\".\"\".\"\".\"component0..*(Slice Definition)Slice: Unordered, Open by pattern:code
\".\"\".\"\".\"\".\"component:gene-studied0..*BackboneElementGene studied ID
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
\".\"\".\"\".\"\".\"\".\"value[x]1..1CodeableConceptBinding: HGNC (extensible)
\".\"\".\"\".\"\".\"component:gene-mutations0..*BackboneElementGene Mutations ID
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 36908-2
\".\"\".\"\".\"\".\"\".\"value[x]1..1CodeableConceptBinding: HGVS (required)
\".\"\".\"\".\"\".\"component:region-description0..*BackboneElementRegion Description
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 81293-3
\".\"\".\"\".\"\".\"\".\"value[x]1..1string
\".\"\".\"\".\"\".\"component:region-coverage0..1BackboneElementRegion Coverage
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: region-coverage
\".\"\".\"\".\"\".\"\".\"value[x]1..1Quantity
\".\"\".\"\".\"\".\"component:ranges-examined0..*BackboneElementRange(s) of DNA sequence examined
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 51959-5
\".\"\".\"\".\"\".\"\".\"value[x]1..1Range
\".\"\".\"\".\"\".\"component:coordinate-system0..1BackboneElementCoordinate System
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
\".\"\".\"\".\"\".\"\".\"value[x]1..1CodeableConcept0-based interval | 0-based character | 1-based character
Binding: LOINC Answer List LL5323-2 (preferred)
\".\"\".\"\".\"\".\"component:genomic-ref-seq0..1BackboneElementGenomic reference sequence ID
\".\"\".\"\".\"\".\"\".\"code1..1CodeableConceptRequired Pattern: At least the following
\".\"\".\"\".\"\".\"\".\"\".\"coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
\".\"\".\"\".\"\".\"\".\"\".\"\".\"system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
\".\"\".\"\".\"\".\"\".\"\".\"\".\"code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
\".\"\".\"\".\"\".\"\".\"value[x]1..1CodeableConceptBinding: (unbound) (example)

\"doco\" Documentation for this format
" }, "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied", "version": "1.0.0", "name": "RegionStudied", "title": "Region Studied", "status": "draft", "experimental": false, "date": "2017-05-20T00:00:00+00:00", "publisher": "HL7 Clinical Genomics WG", "description": "Observation-related profiles", "fhirVersion": "4.0.1", "mapping": [ { "identity": "v2-cg-results", "uri": "http://unknown.org/V2-CG-Results", "name": "V2-CG-Results" }, { "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/uv/genomics-reporting/StructureDefinition/genomics-base", "derivation": "constraint", "snapshot": {}, "differential": { "element": [ { "id": "Observation", "path": "Observation", "short": "Region Studied", "definition": "The Region Studied profile is used to assert actual regions studied for the performed test(s). Intended coverage areas may differ from actual coverage areas (e.g. due to technical limitations during test performance).", "mustSupport": false, "mapping": [ { "identity": "v2-cg-results", "map": "C" } ] }, { "id": "Observation.code", "path": "Observation.code", "short": "Region Studied", "definition": "The panel code that is used to contain the details about the region studied.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "53041-0" } ] }, "mustSupport": false }, { "id": "Observation.valueCodeableConcept", "path": "Observation.valueCodeableConcept", "min": 0, "max": "0", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false }, { "id": "Observation.component", "path": "Observation.component", "slicing": { "discriminator": [ { "type": "pattern", "path": "code" } ], "rules": "open" }, "mustSupport": false }, { "id": "Observation.component:gene-studied", "path": "Observation.component", "sliceName": "gene-studied", "short": "Gene studied ID", "definition": "HUGO Gene Nomenclature Committee (HGNC) identifier for a gene. List the gene(s) examined in full or in part by the study. If the study addresses multiple genes, these can be recorded in multiple gene studied components . The required coding will use the HGNC gene symbol as the display text and HGNC gene ID as the code.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:gene-studied.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48018-6" } ] }, "mustSupport": false }, { "id": "Observation.component:gene-studied.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "extensible", "description": "HGNC: Human Gene Nomenclature Committee", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc" }, "mapping": [ { "identity": "v2-cg-results", "map": "A.4" } ] }, { "id": "Observation.component:gene-mutations", "path": "Observation.component", "sliceName": "gene-mutations", "short": "Gene Mutations ID", "definition": "Gene mutations that were tested for.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:gene-mutations.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "36908-2" } ] }, "mustSupport": false }, { "id": "Observation.component:gene-mutations.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "required", "description": "HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society", "valueSet": "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs" } }, { "id": "Observation.component:region-description", "path": "Observation.component", "sliceName": "region-description", "short": "Region Description", "definition": "Description of region examined.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:region-description.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "81293-3" } ] }, "mustSupport": false }, { "id": "Observation.component:region-description.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "string" } ], "mustSupport": false }, { "id": "Observation.component:region-coverage", "path": "Observation.component", "sliceName": "region-coverage", "short": "Region Coverage", "definition": "When sequencing, what % of the region was covered.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:region-coverage.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes", "code": "region-coverage" } ] }, "mustSupport": false }, { "id": "Observation.component:region-coverage.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Quantity" } ], "mustSupport": false }, { "id": "Observation.component:ranges-examined", "path": "Observation.component", "sliceName": "ranges-examined", "short": "Range(s) of DNA sequence examined", "definition": "This term is used to report the region(s) of interest for sequencing studies as one or more numeric ranges that identify the parts of the reference sequence that are sequenced. These can be recorded as one or more HL7 numeric ranges using repeat delimiters to seperate multiple such ranges.", "min": 0, "max": "*", "mustSupport": false }, { "id": "Observation.component:ranges-examined.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "51959-5" } ] }, "mustSupport": false }, { "id": "Observation.component:ranges-examined.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "Range" } ], "mustSupport": false }, { "id": "Observation.component:coordinate-system", "path": "Observation.component", "sliceName": "coordinate-system", "short": "Coordinate System", "definition": "Base number of coordinate system either 0-based, with inclusive start and exclusive end (called interval), or 1-based, with inclusive start and end. However, two versions of 1-based are in common use.These systems are HGVS 1-based (called variant method) and VCF 1-based (called alignment method). In general, HGVS recommends right-justification and VCF recommends left-justification. However, these systems further address questions such as wheather or not to place an insertion before or after the nucleotide, and, if always placed before the nucleotide, how to handle insertion after the end of the sequence. Additionally, the systems deal with handling boundary effects of numbers between features. For more details see the HGVS and VCF guides.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:coordinate-system.code", "path": "Observation.component.code", "definition": "This captures the base numbering used to calculate base positions in the reported sequence information.", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "92822-6" } ] }, "mustSupport": false }, { "id": "Observation.component:coordinate-system.value[x]", "path": "Observation.component.value[x]", "short": "0-based interval | 0-based character | 1-based character", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "preferred", "description": "Base coordinate systems start and end measurements for variants", "valueSet": "http://loinc.org/vs/LL5323-2" } }, { "id": "Observation.component:genomic-ref-seq", "path": "Observation.component", "sliceName": "genomic-ref-seq", "short": "Genomic reference sequence ID", "definition": "This field carries the ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and non transcribed stretches. For this ID use either the NCBI genomic nucleotide RefSeq IDs with their version number (see: NCBI.NLM.NIH.Gov/RefSeq) or use the LRG identifiers, without transcript (t or p) extensions -- when they become available. (See- Report sponsored by GEN2PHEN at the European Bioinformatics Institute at Hinxton UK April 24-25, 2008).\rThe NCI RefSeq genomic IDs are distinguished by a prefix of\"NG\" for genes from the nuclear chromosomes and prefix of \"NC\" for genes from mitochondria. The LRG Identifiers have a prefix of \"LRG_\" Mitochondrial genes are not in the scope of LRG.", "min": 0, "max": "1", "mustSupport": false }, { "id": "Observation.component:genomic-ref-seq.code", "path": "Observation.component.code", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "patternCodeableConcept": { "coding": [ { "system": "http://loinc.org", "code": "48013-7" } ] }, "mustSupport": false }, { "id": "Observation.component:genomic-ref-seq.value[x]", "path": "Observation.component.value[x]", "min": 1, "max": "1", "type": [ { "code": "CodeableConcept" } ], "mustSupport": false, "binding": { "strength": "example", "description": "Binding not yet defined" }, "mapping": [ { "identity": "v2-cg-results", "map": "B.9" } ] } ] } }