Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
| Draft as of 2024-11-19 |
{
"resourceType" : "ConceptMap",
"id" : "dna-change-type-map",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: ConceptMap dna-change-type-map</b></p><a name=\"dna-change-type-map\"> </a><a name=\"hcdna-change-type-map\"> </a><a name=\"dna-change-type-map-en-US\"> </a><p>Mapping from http://loinc.org/vs/LL379-9 to <a href=\"ValueSet-dna-change-type-vs.html\">DNA Change Type</a></p><br/><p><b>Group 1 </b>Mapping from <a href=\"http://terminology.hl7.org/6.1.0/CodeSystem-v3-loinc.html\">Logical Observation Identifiers, Names and Codes (LOINC)</a> to <a href=\"http://terminology.hl7.org/6.1.0/CodeSystem-SO.html\">Sequence Ontology</a></p><table class=\"grid\"><tr><td><b>Source Code</b></td><td><b>Relationship</b></td><td><b>Target Code</b></td></tr><tr><td>LA9658-1 (Wild type)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:0002073 (no_sequence_alteration)</td></tr><tr><td>LA6692-3 (Deletion)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:0000159 (deletion)</td></tr><tr><td>LA6686-5 (Duplication)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:1000035 (duplication)</td></tr><tr><td>LA6687-3 (Insertion)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:0000667 (insertion)</td></tr><tr><td>LA6688-1 (Insertion/Deletion)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:1000032 (delins)</td></tr><tr><td>LA6689-9 (Inversion)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:1000036 (inversion)</td></tr><tr><td>LA6690-7 (Substitution)</td><td><a href=\"http://hl7.org/fhir/extensions/5.1.0/CodeSystem-concept-map-equivalence.html#equivalent\" title=\"equivalent\">is equivalent to</a></td><td>SO:1000002 (substitution)</td></tr></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/ConceptMap/dna-change-type-map",
"version" : "3.0.0",
"name" : "DNAChangeType",
"title" : "DNA Change Type Map",
"status" : "draft",
"experimental" : false,
"date" : "2024-11-19T22:01:39+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" : "LOINC and SequenceOntology mappings for dna change type",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"copyright" : "This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.",
"sourceCanonical" : "http://loinc.org/vs/LL379-9",
"targetCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs",
"group" : [
{
"source" : "http://loinc.org",
"target" : "http://www.sequenceontology.org",
"element" : [
{
"code" : "LA9658-1",
"display" : "Wild type",
"target" : [
{
"code" : "SO:0002073",
"display" : "no_sequence_alteration",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6692-3",
"display" : "Deletion",
"target" : [
{
"code" : "SO:0000159",
"display" : "deletion",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6686-5",
"display" : "Duplication",
"target" : [
{
"code" : "SO:1000035",
"display" : "duplication",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6687-3",
"display" : "Insertion",
"target" : [
{
"code" : "SO:0000667",
"display" : "insertion",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6688-1",
"display" : "Insertion/Deletion",
"target" : [
{
"code" : "SO:1000032",
"display" : "delins",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6689-9",
"display" : "Inversion",
"target" : [
{
"code" : "SO:1000036",
"display" : "inversion",
"equivalence" : "equivalent"
}
]
},
{
"code" : "LA6690-7",
"display" : "Substitution",
"target" : [
{
"code" : "SO:1000002",
"display" : "substitution",
"equivalence" : "equivalent"
}
]
}
]
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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