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Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
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MolecularSequence example for long fusion RNA molecule of FGFR and MET
@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <https://loinc.org/rdf/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- [a fhir:MolecularSequence ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "seq-ordinal"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"seq-ordinal\"> </a></p><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\">Resource MolecularSequence "seq-ordinal" </p></div><p><b>type</b>: rna</p><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 1</p><p><b>sequenceRange</b>: 1-2194</p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NM_000141.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000141.5)</span></td><td>1</td><td>2194</td></tr></table></blockquote><blockquote><p><b>relative</b></p><p><b>coordinateSystem</b>: 1-based character counting <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA30102-0)</span></p><p><b>ordinalPosition</b>: 2</p><p><b>sequenceRange</b>: 2194-4899</p><h3>StartingSequences</h3><table class=\"grid\"><tr><td>-</td><td><b>Sequence[x]</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NM_000245.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#NM_000245.4)</span></td><td>1923</td><td>6822</td></tr></table></blockquote></div>" ] ; # fhir:type [ fhir:v "rna"] ; # fhir:relative ( [ fhir:coordinateSystem [ fhir:coding ( [ a loinc:LA30102-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA30102-0" ] ; fhir:display [ fhir:v "1-based character counting" ] ] ) ] ; fhir:ordinalPosition [ fhir:v "1"^^xsd:integer ] ; fhir:sequenceRange [ fhir:low [ fhir:value [ fhir:v "1"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "2194"^^xsd:decimal ] ] ] ; fhir:startingSequence [ fhir:sequence [ a fhir:CodeableConcept ; fhir:coding ( [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/nuccore/"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000141.5" ] ] ) ] ; fhir:windowStart [ fhir:v "1"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "2194"^^xsd:integer ] ] ] [ fhir:coordinateSystem [ fhir:coding ( [ a loinc:LA30102-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA30102-0" ] ; fhir:display [ fhir:v "1-based character counting" ] ] ) ] ; fhir:ordinalPosition [ fhir:v "2"^^xsd:integer ] ; fhir:sequenceRange [ fhir:low [ fhir:value [ fhir:v "2194"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "4899"^^xsd:decimal ] ] ] ; fhir:startingSequence [ fhir:sequence [ a fhir:CodeableConcept ; fhir:coding ( [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/nuccore/"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000245.4" ] ] ) ] ; fhir:windowStart [ fhir:v "1923"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "6822"^^xsd:integer ] ] ] )] . # specific edits would be here # -------------------------------------------------------------------------------------
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.
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