Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build
Molecular Definition Implementation Guide for Molecular Data Types
1.0.0-ballot1 - ci-build
Molecular Definition Implementation Guide for Molecular Data Types, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 1.0.0-ballot1 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/molecular-definition-data-types/ and changes regularly. See the Directory of published versions
{
"resourceType" : "MolecularDefinition",
"id" : "example-allelesliced-cyp2c19-661g-coded",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/molecular-definition-data-types/StructureDefinition/allele"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: MolecularDefinition example-allelesliced-cyp2c19-661g-coded</b></p><a name=\"example-allelesliced-cyp2c19-661g-coded\"> </a><a name=\"hcexample-allelesliced-cyp2c19-661g-coded\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-allele.html\">Allele</a></p></div><p><b>moleculeType</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type rna}\">RNA Sequence</span></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type rna}\">RNA Sequence</span></p><blockquote><p><b>location</b></p><blockquote><p><b>sequenceLocation</b></p><p><b>sequenceContext</b>: <a href=\"MolecularDefinition-example-sequence-nm0007694-url.html\">Starting Sequence Resource: (CYP2C19), mRNA, NM_000769.4</a></p><blockquote><p><b>coordinateInterval</b></p><h3>CoordinateSystems</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>System</b></td><td><b>Origin</b></td><td><b>NormalizationMethod</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</span></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/coordinate-origin sequence-start}\">Sequence start</span></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/normalization-method left-shift}\">Left shift</span></td></tr></table><p><b>start</b>: 661</p><p><b>end</b>: 661</p></blockquote><p><b>strand</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/strand-orientation forward}\">Forward strand</span></p></blockquote></blockquote><blockquote><p><b>representation</b></p><p><b>focus</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus allele-state}\">Allele State</span></p><p><b>code</b>: <span title=\"Codes:{http://www.pharmvar.org PV00076}\">CYP2C19*1.002</span></p><h3>Literals</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Value</b></td></tr><tr><td style=\"display: none\">*</td><td>G</td></tr></table></blockquote><blockquote><p><b>representation</b></p><p><b>focus</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus context-state}\">Context State</span></p><h3>Literals</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Value</b></td></tr><tr><td style=\"display: none\">*</td><td>G</td></tr></table></blockquote></div>"
},
"moleculeType" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type",
"code" : "rna",
"display" : "RNA Sequence"
}
]
},
"type" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecule-type",
"code" : "rna",
"display" : "RNA Sequence"
}
]
}
],
"location" : [
{
"sequenceLocation" : {
"sequenceContext" : {
🔗 "reference" : "MolecularDefinition/example-sequence-nm0007694-url",
"type" : "MolecularDefinition",
"display" : "Starting Sequence Resource: (CYP2C19), mRNA, NM_000769.4"
},
"coordinateInterval" : {
"coordinateSystem" : {
"system" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA30102-0",
"display" : "1-based character counting"
}
]
},
"origin" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/coordinate-origin",
"code" : "sequence-start",
"display" : "Sequence start"
}
]
},
"normalizationMethod" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/normalization-method",
"code" : "left-shift",
"display" : "Left shift"
}
]
}
},
"startQuantity" : {
"value" : 661
},
"endQuantity" : {
"value" : 661
}
},
"strand" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/strand-orientation",
"code" : "forward",
"display" : "Forward strand"
}
]
}
}
}
],
"representation" : [
{
"focus" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus",
"code" : "allele-state",
"display" : "Allele State"
}
]
},
"code" : [
{
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "PV00076",
"display" : "CYP2C19*1.002"
}
]
}
],
"literal" : {
"value" : "G"
}
},
{
"focus" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/molecular-definition-data-types/CodeSystem/molecular-definition-focus",
"code" : "context-state",
"display" : "Context State"
}
]
},
"literal" : {
"value" : "G"
}
}
]
}