Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Find Subject Molecular Consequences - JSON Representation

Active as of 2024-04-09

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{
  "resourceType" : "OperationDefinition",
  "id" : "find-subject-molecular-consequences",
  "text" : {
    "status" : "extensions",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>Parameters</p><table class=\"grid\"><tr><td><b>Use</b></td><td><b>Name</b></td><td><b>Scope</b></td><td><b>Cardinality</b></td><td><b>Type</b></td><td><b>Binding</b></td><td><b>Documentation</b></td></tr><tr><td>IN</td><td>subject</td><td/><td>1..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#reference\">reference</a>)</td><td/><td><div><p>The subject of interest.</p>\n</div></td></tr><tr><td>IN</td><td>variants</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#string\">string</a>)</td><td/><td><div><p>List of variants from which consequences are derived. Must be in HGVS or SPDI format.</p>\n</div></td></tr><tr><td>IN</td><td>ranges</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#special\">special</a>)</td><td/><td><div><p>List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820').</p>\n</div></td></tr><tr><td>IN</td><td>featureConsequences</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#token\">token</a>)</td><td/><td><div><p>List of consequences sought. Must be in token or codesystem|code format. (These will generally be coded with Sequence Ontology codes under SO:0001537)</p>\n</div></td></tr><tr><td>IN</td><td>testIdentifiers</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#token\">token</a>)</td><td/><td><div><p>Supply a list of test identifiers. Only results originating from one of these tests will be returned.</p>\n</div></td></tr><tr><td>IN</td><td>testDateRange</td><td/><td>0..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#Period\">Period</a></td><td/><td><div><p>Supply a date range. Only results generated during this range will be returned.</p>\n</div></td></tr><tr><td>IN</td><td>specimenIdentifiers</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#token\">token</a>)</td><td/><td><div><p>Supply a list of specimen identifiers. Only results derived from one of these specimens will be returned.</p>\n</div></td></tr><tr><td>IN</td><td>genomicSourceClass</td><td/><td>0..1</td><td><a href=\"http://hl7.org/fhir/R4/datatypes.html#string\">string</a><br/>(<a href=\"http://hl7.org/fhir/R4/search.html#token\">token</a>)</td><td/><td><div><p>Enables an App to limit results to those that are 'germline' or 'somatic'. Default is to include variants irrespective of genomic source class.</p>\n</div></td></tr><tr><td>OUT</td><td>consequence</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/observation.html\">Observation</a></td><td/><td><div><p>Consequences must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence]. The target(s) of the consequence's derivedFrom shall also be included in the response.</p>\n</div></td></tr><tr><td>OUT</td><td>variant</td><td/><td>0..*</td><td><a href=\"http://hl7.org/fhir/R4/observation.html\">Observation</a></td><td/><td><div><p>Variants must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant].</p>\n</div></td></tr></table></div>"
  },
  "extension" : [
    {
      "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode" : "cg"
    }
  ],
  "url" : "http://hl7.org/fhir/uv/genomics-reporting/OperationDefinition/find-subject-molecular-consequences",
  "version" : "3.0.1-SNAPSHOT",
  "name" : "FindSubjectMolecularConsequences",
  "title" : "Find Subject Molecular Consequences",
  "status" : "active",
  "kind" : "operation",
  "date" : "2024-04-09T13:57:55+00:00",
  "publisher" : "HL7 International / Clinical Genomics",
  "contact" : [
    {
      "name" : "HL7 International / Clinical Genomics",
      "telecom" : [
        {
          "system" : "url",
          "value" : "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system" : "email",
          "value" : "cg@lists.HL7.org"
        }
      ]
    }
  ],
  "description" : "Retrieves molecular consequences of a DNA variant.",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "code" : "match",
  "system" : false,
  "type" : true,
  "instance" : false,
  "parameter" : [
    {
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      "use" : "in",
      "min" : 1,
      "max" : "1",
      "documentation" : "The subject of interest.",
      "type" : "string",
      "searchType" : "reference"
    },
    {
      "name" : "variants",
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      "min" : 0,
      "max" : "*",
      "documentation" : "List of variants from which consequences are derived. Must be in HGVS or SPDI format.",
      "type" : "string",
      "searchType" : "string"
    },
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      "use" : "in",
      "min" : 0,
      "max" : "*",
      "documentation" : "List of regions to be searched for variants. Must be in zero-based RefSeq:Integer-range format (e.g. 'NC_000007.14:55174721-55174820').",
      "type" : "string",
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    },
    {
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      "min" : 0,
      "max" : "*",
      "documentation" : "List of consequences sought. Must be in token or codesystem|code format. (These will generally be coded with Sequence Ontology codes under SO:0001537)",
      "type" : "string",
      "searchType" : "token"
    },
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    },
    {
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      "use" : "in",
      "min" : 0,
      "max" : "1",
      "documentation" : "Supply a date range. Only results generated during this range will be returned.",
      "type" : "Period"
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    },
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      "searchType" : "token"
    },
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          "valueUri" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
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      ],
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      "min" : 0,
      "max" : "*",
      "documentation" : "Consequences must conform to [Profile: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence]. The target(s) of the consequence's derivedFrom shall also be included in the response.",
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