{
  "description": "FHIR implementation guide for the Genomics Clinical Picture Repository standard developed as part of the Standardised Clinical Phenotypes project in Australian Genomics.",
  "_filename": "ImplementationGuide-agha.fhir.genclipr.json",
  "package_name": "agha.fhir.genclipr",
  "definition": {
    "page": {
      "page": [ {
        "title": "Overview",
        "nameUrl": "index.html",
        "generation": "markdown"
      }, {
        "title": "Downloads",
        "nameUrl": "downloads.html",
        "generation": "markdown"
      }, {
        "page": [ {
          "title": "Biological Sex",
          "nameUrl": "StructureDefinition-BiologicalSex.html",
          "generation": "generated"
        }, {
          "title": "Deidentified Patient",
          "nameUrl": "StructureDefinition-DeidentifiedPatient.html",
          "generation": "generated"
        }, {
          "title": "Examination Finding",
          "nameUrl": "StructureDefinition-ExaminationFinding.html",
          "generation": "generated"
        }, {
          "title": "Finding",
          "nameUrl": "StructureDefinition-Finding.html",
          "generation": "generated"
        }, {
          "title": "Genomics Clinical Picture Repository Encounter",
          "nameUrl": "StructureDefinition-GencliprEncounter.html",
          "generation": "generated"
        }, {
          "title": "Genomics Clinical Picture Repository Research Study",
          "nameUrl": "StructureDefinition-GencliprResearchStudy.html",
          "generation": "generated"
        }, {
          "title": "Genomics Clinical Picture Repository Research Subject",
          "nameUrl": "StructureDefinition-GencliprResearchSubject.html",
          "generation": "generated"
        }, {
          "title": "Genomics Clinical Picture Repository Service Request",
          "nameUrl": "StructureDefinition-GencliprServiceRequest.html",
          "generation": "generated"
        }, {
          "title": "Imaging Finding",
          "nameUrl": "StructureDefinition-ImagingFinding.html",
          "generation": "generated"
        }, {
          "title": "Laboratory Finding",
          "nameUrl": "StructureDefinition-LaboratoryFinding.html",
          "generation": "generated"
        }, {
          "title": "Sign",
          "nameUrl": "StructureDefinition-Sign.html",
          "generation": "generated"
        }, {
          "title": "Symptom",
          "nameUrl": "StructureDefinition-Symptom.html",
          "generation": "generated"
        }, {
          "title": "Abnormal Clinical Findings Value Set",
          "nameUrl": "ValueSet-AbnormalClinicalFindings.html",
          "generation": "generated"
        }, {
          "title": "Biological Sexes Value Set",
          "nameUrl": "ValueSet-BiologicalSexes.html",
          "generation": "generated"
        }, {
          "title": "Encounter Class Value Set",
          "nameUrl": "ValueSet-EncounterClasses.html",
          "generation": "generated"
        }, {
          "title": "Encounter Type Value Set",
          "nameUrl": "ValueSet-EncounterTypes.html",
          "generation": "generated"
        }, {
          "title": "Genomic Test Types Value Set",
          "nameUrl": "ValueSet-GenomicTestTypes.html",
          "generation": "generated"
        }, {
          "title": "Lateralities Value Set",
          "nameUrl": "ValueSet-Lateralities.html",
          "generation": "generated"
        }, {
          "title": "Presence Value Set",
          "nameUrl": "ValueSet-PresenceValues.html",
          "generation": "generated"
        }, {
          "title": "Severity Value Set",
          "nameUrl": "ValueSet-Severities.html",
          "generation": "generated"
        }, {
          "title": "Test Interpretation Value Set",
          "nameUrl": "ValueSet-TestInterpretationValues.html",
          "generation": "generated"
        }, {
          "title": "Encounter Class",
          "nameUrl": "CodeSystem-EncounterClass.html",
          "generation": "generated"
        }, {
          "title": "Encounter Type",
          "nameUrl": "CodeSystem-EncounterType.html",
          "generation": "generated"
        }, {
          "title": "Finding Type",
          "nameUrl": "CodeSystem-FindingType.html",
          "generation": "generated"
        }, {
          "title": "Genomic Test Type",
          "nameUrl": "CodeSystem-GenomicTestType.html",
          "generation": "generated"
        }, {
          "title": "Identifier Type",
          "nameUrl": "CodeSystem-IdentifierType.html",
          "generation": "generated"
        }, {
          "title": "Mitochondrial Findings",
          "nameUrl": "CodeSystem-MitochondrialFindings.html",
          "generation": "generated"
        } ],
        "title": "Artifacts Summary",
        "nameUrl": "artifacts.html",
        "generation": "html"
      } ],
      "title": "Table of Contents",
      "nameUrl": "toc.html",
      "generation": "html"
    },
    "grouping": [ {
      "id": "-str-profile",
      "name": "Structures: Resource Profiles",
      "description": "These define constraints on FHIR resources for systems conforming to this implementation guide"
    }, {
      "id": "-term-valueset",
      "name": "Terminology: Value Sets",
      "description": "These define sets of codes used by systems conforming to this implementation guide"
    }, {
      "id": "-term-codesystem",
      "name": "Terminology: Code Systems",
      "description": "These define new code systems used by systems conforming to this implementation guide"
    } ],
    "resource": [ {
      "name": "Biological Sex",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-BiologicalSex.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/BiologicalSex"
      },
      "groupingId": "-str-profile",
      "description": "An observation that represents the biological sex of a patient.",
      "exampleBoolean": false
    }, {
      "name": "Deidentified Patient",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-DeidentifiedPatient.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/DeidentifiedPatient"
      },
      "groupingId": "-str-profile",
      "description": "A deidentified patient whose clinical picture is being stored in the repository.",
      "exampleBoolean": false
    }, {
      "name": "Examination Finding",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-ExaminationFinding.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/ExaminationFinding"
      },
      "groupingId": "-str-profile",
      "description": "An observation made by a clinician or patient that can be normal or abnormal.",
      "exampleBoolean": false
    }, {
      "name": "Finding",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-Finding.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/Finding"
      },
      "groupingId": "-str-profile",
      "description": "An observation about a patient that can be normal or abnormal and is expressed in a way that its action is reduced to a single concept (see pattern 3 in http://hl7.org/fhir/R4/observation.html#code-interop).",
      "exampleBoolean": false
    }, {
      "name": "Genomics Clinical Picture Repository Encounter",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-GencliprEncounter.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/GencliprEncounter"
      },
      "groupingId": "-str-profile",
      "description": "An encounter stored in the repository.",
      "exampleBoolean": false
    }, {
      "name": "Genomics Clinical Picture Repository Research Study",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-GencliprResearchStudy.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/GencliprResearchStudy"
      },
      "groupingId": "-str-profile",
      "description": "Captures information about a research study and groups encounters that where generated as part of the study.",
      "exampleBoolean": false
    }, {
      "name": "Genomics Clinical Picture Repository Research Subject",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-GencliprResearchSubject.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/GencliprResearchSubject"
      },
      "groupingId": "-str-profile",
      "description": "This resource represents a patient that is the subject of a research study.",
      "exampleBoolean": false
    }, {
      "name": "Genomics Clinical Picture Repository Service Request",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-GencliprServiceRequest.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/GencliprServiceRequest"
      },
      "groupingId": "-str-profile",
      "description": "Captues information about the genomic testing requested for a patient.",
      "exampleBoolean": false
    }, {
      "name": "Imaging Finding",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-ImagingFinding.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/ImagingFinding"
      },
      "groupingId": "-str-profile",
      "description": "An observation based on the result of an imaging study.",
      "exampleBoolean": false
    }, {
      "name": "Laboratory Finding",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-LaboratoryFinding.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/LaboratoryFinding"
      },
      "groupingId": "-str-profile",
      "description": "An observation based on the result of a laboratory test.",
      "exampleBoolean": false
    }, {
      "name": "Sign",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-Sign.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/Sign"
      },
      "groupingId": "-str-profile",
      "description": "A sign is a bodily feature of a patient observed by a clinician which is deemed to be of clinical relevance. It records a phenotype that is clinically abnormal.",
      "exampleBoolean": false
    }, {
      "name": "Symptom",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "StructureDefinition-Symptom.html"
      } ],
      "reference": {
        "reference": "StructureDefinition/Symptom"
      },
      "groupingId": "-str-profile",
      "description": "A symptom is an observation made by the patient and is hypothesized to be a realization of a disease.",
      "exampleBoolean": false
    }, {
      "name": "Abnormal Clinical Findings Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-AbnormalClinicalFindings.html"
      } ],
      "reference": {
        "reference": "ValueSet/AbnormalClinicalFindings"
      },
      "groupingId": "-term-valueset",
      "description": "Abnormal clinical findings.",
      "exampleBoolean": false
    }, {
      "name": "Biological Sexes Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-BiologicalSexes.html"
      } ],
      "reference": {
        "reference": "ValueSet/BiologicalSexes"
      },
      "groupingId": "-term-valueset",
      "description": "SNOMED CT concepts for biological sex.",
      "exampleBoolean": false
    }, {
      "name": "Encounter Class Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-EncounterClasses.html"
      } ],
      "reference": {
        "reference": "ValueSet/EncounterClasses"
      },
      "groupingId": "-term-valueset",
      "description": "Classes of encounters captured in a genomics clinical picture FHIR repository.",
      "exampleBoolean": false
    }, {
      "name": "Encounter Type Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-EncounterTypes.html"
      } ],
      "reference": {
        "reference": "ValueSet/EncounterTypes"
      },
      "groupingId": "-term-valueset",
      "description": "Types of encounters captured in a genomics clinical picture FHIR repository.",
      "exampleBoolean": false
    }, {
      "name": "Genomic Test Types Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-GenomicTestTypes.html"
      } ],
      "reference": {
        "reference": "ValueSet/GenomicTestTypes"
      },
      "groupingId": "-term-valueset",
      "description": "Genomic test types, including research tests.",
      "exampleBoolean": false
    }, {
      "name": "Lateralities Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-Lateralities.html"
      } ],
      "reference": {
        "reference": "ValueSet/Lateralities"
      },
      "groupingId": "-term-valueset",
      "description": "Codes used to describe the laterality of a body structure.",
      "exampleBoolean": false
    }, {
      "name": "Presence Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-PresenceValues.html"
      } ],
      "reference": {
        "reference": "ValueSet/PresenceValues"
      },
      "groupingId": "-term-valueset",
      "description": "Presence / absence values from SNOMED CT.",
      "exampleBoolean": false
    }, {
      "name": "Severity Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-Severities.html"
      } ],
      "reference": {
        "reference": "ValueSet/Severities"
      },
      "groupingId": "-term-valueset",
      "description": "Codes used to describe the severity of a finding.",
      "exampleBoolean": false
    }, {
      "name": "Test Interpretation Value Set",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "ValueSet-TestInterpretationValues.html"
      } ],
      "reference": {
        "reference": "ValueSet/TestInterpretationValues"
      },
      "groupingId": "-term-valueset",
      "description": "Test interpretation values from SNOMED CT.",
      "exampleBoolean": false
    }, {
      "name": "Encounter Class",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-EncounterClass.html"
      } ],
      "reference": {
        "reference": "CodeSystem/EncounterClass"
      },
      "groupingId": "-term-codesystem",
      "description": "Class of encounters captured in a genomics clinical picture FHIR repository.",
      "exampleBoolean": false
    }, {
      "name": "Encounter Type",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-EncounterType.html"
      } ],
      "reference": {
        "reference": "CodeSystem/EncounterType"
      },
      "groupingId": "-term-codesystem",
      "description": "Type of encounters captured in a genomics clinical picture FHIR repository.",
      "exampleBoolean": false
    }, {
      "name": "Finding Type",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-FindingType.html"
      } ],
      "reference": {
        "reference": "CodeSystem/FindingType"
      },
      "groupingId": "-term-codesystem",
      "description": "Extends the Observation Category codes to include additional categories.",
      "exampleBoolean": false
    }, {
      "name": "Genomic Test Type",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-GenomicTestType.html"
      } ],
      "reference": {
        "reference": "CodeSystem/GenomicTestType"
      },
      "groupingId": "-term-codesystem",
      "description": "Types of genomic tests not available in LOINC.",
      "exampleBoolean": false
    }, {
      "name": "Identifier Type",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-IdentifierType.html"
      } ],
      "reference": {
        "reference": "CodeSystem/IdentifierType"
      },
      "groupingId": "-term-codesystem",
      "description": "Types of identifiers used in a genomics clinical picture FHIR repository.",
      "exampleBoolean": false
    }, {
      "name": "Mitochondrial Findings",
      "extension": [ {
        "url": "http://hl7.org/fhir/StructureDefinition/implementationguide-page",
        "valueUri": "CodeSystem-MitochondrialFindings.html"
      } ],
      "reference": {
        "reference": "CodeSystem/MitochondrialFindings"
      },
      "groupingId": "-term-codesystem",
      "description": "Mitochondrial-related findings that are not in HPO or SNOMED CT.",
      "exampleBoolean": false
    } ],
    "extension": [ {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "copyrightyear"
      }, {
        "url": "value",
        "valueString": "2021+"
      } ]
    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "releaselabel"
      }, {
        "url": "value",
        "valueString": "ci-build"
      } ]
    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "path-liquid"
      }, {
        "url": "value",
        "valueString": "template/liquid"
      } ]
    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "path-liquid"
      }, {
        "url": "value",
        "valueString": "input/liquid"
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    }, {
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      "extension": [ {
        "url": "code",
        "valueString": "path-qa"
      }, {
        "url": "value",
        "valueString": "temp/qa"
      } ]
    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "path-temp"
      }, {
        "url": "value",
        "valueString": "temp/pages"
      } ]
    }, {
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        "valueString": "path-output"
      }, {
        "url": "value",
        "valueString": "output"
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    }, {
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      "extension": [ {
        "url": "code",
        "valueString": "path-suppressed-warnings"
      }, {
        "url": "value",
        "valueString": "input/ignoreWarnings.txt"
      } ]
    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "path-history"
      }, {
        "url": "value",
        "valueString": "http://aehrc.github.io/genclipr-fhir-ig/history.html"
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    }, {
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      "extension": [ {
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        "valueString": "template-md"
      }, {
        "url": "value",
        "valueString": "template-page-md.html"
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      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "apply-contact"
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        "url": "value",
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        "url": "value",
        "valueString": "true"
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    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
        "url": "code",
        "valueString": "apply-copyright"
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        "url": "value",
        "valueString": "true"
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    }, {
      "url": "http://hl7.org/fhir/tools/StructureDefinition/ig-parameter",
      "extension": [ {
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        "valueString": "apply-jurisdiction"
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        "url": "value",
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        "url": "code",
        "valueString": "propagate-status"
      }, {
        "url": "value",
        "valueString": "true"
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    } ],
    "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"
    } ]
  },
  "date": "2022-03-21T00:46:36+00:00",
  "publisher": "The Australian e-Health Research Centre",
  "fhirVersion": [ "4.0.1" ],
  "license": "CC0-1.0",
  "dependsOn": [ {
    "id": "hl7_fhir_uv_genomics_reporting",
    "uri": "http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/hl7.fhir.uv.genomics-reporting",
    "version": "1.0.0",
    "packageId": "hl7.fhir.uv.genomics-reporting"
  } ],
  "name": "GenomicsClinicalPictureRepositoryIG",
  "copyright": "[Australian Genomics](https://www.australiangenomics.org.au)",
  "type": null,
  "experimental": null,
  "resourceType": "ImplementationGuide",
  "title": "Genomics Clinical Picture Repository Implementation Guide",
  "package_version": "0.1.0",
  "status": "draft",
  "id": "8e4daef5-aec5-4965-8e67-eed830ed3917",
  "kind": null,
  "url": "http://aehrc.github.io/genclipr-fhir-ig/ImplementationGuide/agha.fhir.genclipr",
  "version": "0.1.0",
  "packageId": "agha.fhir.genclipr",
  "contact": [ {
    "name": "The Australian e-Health Research Centre",
    "telecom": [ {
      "value": "https://aehrc.com",
      "system": "url"
    }, {
      "value": "ontoserver-support@csiro.au",
      "system": "email"
    } ]
  } ]
}