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.