HL7.TERMINOLOGY\Locus Reference Genomic Sequences (LRG) - XML Representation

This page is part of the HL7 Terminology (v2.1.0: Release) based on FHIR R4. The current version which supercedes this version is 5.2.0. For a full list of available versions, see the Directory of published versions
: Locus Reference Genomic Sequences (LRG) - XML Representation

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<NamingSystem xmlns="http://hl7.org/fhir">
  <id value="v3-lrg"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><h3>Summary</h3><table class="grid"><tr><td>Defining URL</td><td>http://terminology.hl7.org/NamingSystem/v3-lrg</td></tr><tr><td>Name</td><td>Lrg</td></tr><tr><td>Status</td><td>active</td></tr><tr><td>Definition</td><td><div><p>In collaboration with NCBI, the European Bioinformatics Institute (EBI) is developing the Locus Reference Genomic Sequences (LRG) database, which is a database of reference sequences.</p>
<p>LRG is a system for providing a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. LRG is not a nomenclature system. More than one LRG could be created for a region of interest, should that need arise. Additional annotations will be present that may change with time (each item carrying its own date stamp), so that the latest ancillary knowledge about a gene is directly available. In other words, an LRG sequence and its core annotation are not meant to represent current biology knowledge, but to provide a standard for reporting variation in a stable coordinate system. The combination of the LRG plus the updatable-annotation layer will be used to support the biological interpretation of variants.</p>
<p>LRG identifiers can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type will be gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, LRG identifiers can be used to as the observation values for Genomic Reference Sequence Identifier (LOINC code: 48013-7).</p>
<p>LRG is a database that can be used freely by the public.</p>
</div></td></tr><tr><td>Publisher</td><td>HL7</td></tr></table><h3>Identifiers</h3><table class="grid"><tr><td><b>Type</b></td><td><b>Value</b></td><td><b>Preferred</b></td></tr><tr><td>OID</td><td>2.16.840.1.113883.6.283</td><td>true</td></tr><tr><td>URI</td><td>http://www.lrg-sequence.org</td><td>true</td></tr></table></div>
  </text>
  <extension url="http://hl7.org/fhir/tools/StructureDefinition/extension-title">
    <valueString value="Locus Reference Genomic Sequences (LRG)"/>
  </extension>
  <extension
             url="http://hl7.org/fhir/5.0/StructureDefinition/extension-NamingSystem.url">
    <valueUri value="http://terminology.hl7.org/NamingSystem/v3-lrg"/>
  </extension>
  <extension
             url="http://terminology.hl7.org/StructureDefinition/ext-namingsystem-version">
    <valueString value="2.1.0"/>
  </extension>
  <name value="Lrg"/>
  <status value="active"/>
  <kind value="codesystem"/>
  <date value="2019-03-20T00:00:00-04:00"/>
  <publisher value="HL7"/>
  <contact>
    <name value="Wellcome Trust"/>
  </contact>
  <responsible value="HL7"/>
  <description
               value="In collaboration with NCBI, the European Bioinformatics Institute (EBI) is developing the Locus Reference Genomic Sequences (LRG) database, which is a database of reference sequences.

LRG is a system for providing a genomic DNA sequence representation of a single gene that is idealized, has a permanent ID (with no versioning), and core content that never changes. LRG is not a nomenclature system. More than one LRG could be created for a region of interest, should that need arise. Additional annotations will be present that may change with time (each item carrying its own date stamp), so that the latest ancillary knowledge about a gene is directly available. In other words, an LRG sequence and its core annotation are not meant to represent current biology knowledge, but to provide a standard for reporting variation in a stable coordinate system. The combination of the LRG plus the updatable-annotation layer will be used to support the biological interpretation of variants.

LRG identifiers can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type will be gene symbols can be used with the HL7 coded data type. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, LRG identifiers can be used to as the observation values for Genomic Reference Sequence Identifier (LOINC code: 48013-7).

LRG is a database that can be used freely by the public."/>
  <uniqueId>
    <type value="oid"/>
    <value value="2.16.840.1.113883.6.283"/>
    <preferred value="true"/>
  </uniqueId>
  <uniqueId>
    <type value="uri"/>
    <value value="http://www.lrg-sequence.org"/>
    <preferred value="true"/>
  </uniqueId>
</NamingSystem>