This page is part of the FHIR Specification (v5.0.0-ballot: FHIR R5 Ballot Preview). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3
Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
Raw JSON (canonical form + also see JSON Format Specification)
Example of a record with 1-based coordinatesystem
{ "resourceType": "MolecularSequence", "id": "coord-1-base", "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MolecularSequence</b><a name=\"coord-1-base\"> </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 "coord-1-base" </p></div><p><b>type</b>: dna</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><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><td><b>Strand</b></td></tr><tr><td>*</td><td>ACGTAGTC</td><td>1</td><td>8</td><td>watson</td></tr></table><blockquote><p><b>edit</b></p><p><b>start</b>: 2</p><p><b>end</b>: 3</p><p><b>replacementSequence</b>: ATG</p><p><b>replacedSequence</b>: -</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 5</p><p><b>end</b>: 5</p><p><b>replacementSequence</b>: T</p><p><b>replacedSequence</b>: A</p></blockquote><blockquote><p><b>edit</b></p><p><b>start</b>: 7</p><p><b>end</b>: 7</p><p><b>replacementSequence</b>: -</p><p><b>replacedSequence</b>: T</p></blockquote></blockquote></div>" }, "type": "dna", "relative": [ { "coordinateSystem": { "coding": [ { "system": "http://loinc.org", "code": "LA30102-0", "display": "1-based character counting" } ] }, "startingSequence": { "sequenceString": "ACGTAGTC", "windowStart": 1, "windowEnd": 8, "strand": "watson" }, "edit": [ { "start": 2, "end": 3, "replacementSequence": "ATG", "replacedSequence": "-" }, { "start": 5, "end": 5, "replacementSequence": "T", "replacedSequence": "A" }, { "start": 7, "end": 7, "replacementSequence": "-", "replacedSequence": "T" } ] } ] }
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.