Release 4 R5 Final QA

This page is part of the FHIR Specification (v4.0.1: R4 (v5.0.0-draft-final: Final QA Preview for R5 - Mixed Normative and STU see ballot notes ) in it's permanent home (it will always be available at this URL). ). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3 R2

Coord-1base-example.json

Example ValueSet/provenance-entity-role (JSON)

Clinical Genomics Terminology Infrastructure Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

Raw JSON ( canonical form + also see JSON Format Specification )

Example of a record with 1-based coordinatesystem Definition for Value SetProvenance Entity Role

{
  "resourceType": "MolecularSequence",
  "id": "coord-1-base",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: coord-1-base</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 1</p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqString</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>watson</td><td>1</td><td>8</td></tr></table><blockquote><p><b>variant</b></p><p><b>start</b>: 2</p><p><b>end</b>: 3</p><p><b>observedAllele</b>: ATG</p><p><b>referenceAllele</b>: -</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 5</p><p><b>end</b>: 5</p><p><b>observedAllele</b>: T</p><p><b>referenceAllele</b>: A</p><p><b>cigar</b>: 3I</p></blockquote><blockquote><p><b>variant</b></p><p><b>start</b>: 7</p><p><b>end</b>: 7</p><p><b>observedAllele</b>: -</p><p><b>referenceAllele</b>: T</p><p><b>cigar</b>: 1D</p></blockquote><p><b>observedSeq</b>: ACATGGTAGC</p></div>"

  "resourceType" : "ValueSet",
  "id" : "provenance-entity-role",
  "meta" : {
    "lastUpdated" : "2023-03-01T23:03:57.298+11:00",
    "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablevalueset"]

  },
  "type": "dna",
  "coordinateSystem": 1,
  "referenceSeq": {
    "referenceSeqString": "ACGTAGTC",
    "strand": "watson",
    "windowStart": 1,
    "windowEnd": 8

  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><ul><li>Include all codes defined in <a href=\"codesystem-provenance-entity-role.html\"><code>http://hl7.org/fhir/provenance-entity-role</code></a></li></ul></div>"

  },
  "variant": [
    {
      "start": 2,
      "end": 3,
      "observedAllele": "ATG",
      "referenceAllele": "-",
      "cigar": "3I"
    },
    {
      "start": 5,
      "end": 5,
      "observedAllele": "T",
      "referenceAllele": "A",
      "cigar": "3I"

  "extension" : [{
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
    "valueCode" : "sec"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
    "valueCode" : "trial-use"
  },
  {
    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
    "valueInteger" : 3
  }],
  "url" : "http://hl7.org/fhir/ValueSet/provenance-entity-role",
  "identifier" : [{
    "system" : "urn:ietf:rfc:3986",
    "value" : "urn:oid:2.16.840.1.113883.4.642.3.436"
  },
  {
    "use" : "old",
    "system" : "urn:ietf:rfc:3986",
    "value" : "urn:oid:2.16.840.1.113883.4.642.3.427"
  },
  {
    "use" : "old",
    "system" : "urn:ietf:rfc:3986",
    "value" : "urn:oid:2.16.840.1.113883.4.642.2.247"
  }],
  "version" : "5.0.0-draft-final",
  "name" : "ProvenanceEntityRole",
  "title" : "Provenance Entity Role",
  "status" : "draft",
  "experimental" : false,
  "date" : "2020-12-28T16:55:11+11:00",
  "publisher" : "HL7 (FHIR Project)",
  "contact" : [{
    "telecom" : [{
      "system" : "url",
      "value" : "http://hl7.org/fhir"

    },
    {
      "start": 7,
      "end": 7,
      "observedAllele": "-",
      "referenceAllele": "T",
      "cigar": "1D"
    }
  ],
  "observedSeq": "ACATGGTAGC"

      "system" : "email",
      "value" : "fhir@lists.hl7.org"
    }]
  }],
  "description" : "How an entity was used in an activity.",
  "jurisdiction" : [{
    "coding" : [{
      "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
      "code" : "001",
      "display" : "World"
    }]
  }],
  "immutable" : true,
  "compose" : {
    "include" : [{
      "system" : "http://hl7.org/fhir/provenance-entity-role"
    }]
  }

}

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.