FHIR IG analytics

Resources that use this resource

Resources that this resource uses

No resources found

Narrative

Note: links and images are rebased to the (stated) source

Source1

{
  "resourceType": "CodeSystem",
  "id": "coordinatesystem-origin",
  "meta": {
    "lastUpdated": "2026-03-13T00:00:00Z",
    "profile": [
      "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode": "cg"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode": "informative"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger": 0
    }
  ],
  "url": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin",
  "identifier": [
    {
      "system": "urn:ietf:rfc:3986",
      "value": "urn:oid:2.16.840.1.113883.4.642.4.3004"
    }
  ],
  "version": "0.1.0-ci-build",
  "name": "CoordinateSystemOrigin",
  "title": "Coordinate System Origin CodeSystem",
  "status": "draft",
  "experimental": true,
  "date": "2026-03-13",
  "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": "clingenomics@lists.hl7.org"
        }
      ]
    }
  ],
  "description": "The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This identifies the conceptual anchor point on the molecule where numbering begins, independent of whether numbering is 0-based or 1-based (which is captured in coordinateSystem.system). No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group.",
  "jurisdiction": [
    {
      "coding": [
        {
          "system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code": "001",
          "display": "World"
        }
      ]
    }
  ],
  "caseSensitive": true,
  "valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-origin",
  "content": "complete",
  "concept": [
    {
      "code": "sequence-start",
      "display": "Sequence Start",
      "definition": "Coordinates are measured from the start of the molecule: the 5' end of a nucleotide sequence or the N-terminus of a polypeptide. This is the default for genomic, chromosomal, and transcript-level coordinate systems (e.g., NC_ or NG_ accession-based positions)."
    },
    {
      "code": "cds-start",
      "display": "CDS Start (A of ATG)",
      "definition": "Coordinates are measured from the adenine of the translation initiation codon (A of ATG = position 1, or 0 in 0-based systems). This is the origin used by the HGVS coding DNA reference sequence (c. prefix). Positions upstream of the ATG are negative (5' UTR); positions downstream of the stop codon are marked with an asterisk (3' UTR)."
    },
    {
      "code": "feature-start",
      "display": "Feature Start",
      "definition": "Coordinates are measured from the start of a named genomic feature, such as the first base of an exon. This is used for HGVS exon-relative or feature-relative position expressions."
    },
    {
      "code": "feature-end",
      "display": "Feature End",
      "definition": "Coordinates are measured from the end of a named genomic feature, such as the last base of an exon. A positive offset extends into the downstream intron; a negative offset extends upstream into the exon. This origin is used for HGVS intronic positions (e.g., c.100+3, where 100 is the last coding base and +3 is the offset into the intron)."
    }
  ]
}