@prefix fhir: . @prefix owl: . @prefix rdf: . @prefix rdfs: . @prefix xsd: . # - resource ------------------------------------------------------------------- a fhir:CodeSystem ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "coordinatesystem-origin"] ; # fhir:meta [ fhir:lastUpdated [ fhir:v "2026-03-13T00:00:00Z"^^xsd:dateTime ] ; fhir:profile ( [ fhir:v "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"^^xsd:anyURI ; fhir:l ] ) ] ; # fhir:language [ fhir:v "en"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div [ fhir:v "

Generated Narrative: CodeSystem coordinatesystem-origin

Last updated: 2026-03-13 00:00:00+0000

Profile: Shareable CodeSystem

This case-sensitive code system http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin defines the following codes:

CodeDisplayDefinition
sequence-start Sequence StartCoordinates 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).
cds-start CDS Start (A of ATG)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).
feature-start Feature StartCoordinates 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.
feature-end Feature EndCoordinates 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).
"^^rdf:XMLLiteral ] ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ; fhir:l ] ; fhir:value [ a fhir:Code ; fhir:v "cg" ] ] [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ; fhir:l ] ; fhir:value [ a fhir:Code ; fhir:v "informative" ] ] [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ; fhir:l ] ; fhir:value [ a fhir:Integer ; fhir:v 0 ] ] ) ; # fhir:url [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin"^^xsd:anyURI ; fhir:l ] ; # fhir:identifier ( [ fhir:system [ fhir:v "urn:ietf:rfc:3986"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:oid:2.16.840.1.113883.4.642.4.3004" ] ] ) ; # fhir:version [ fhir:v "0.1.0-ci-build"] ; # fhir:name [ fhir:v "CoordinateSystemOrigin"] ; # fhir:title [ fhir:v "Coordinate System Origin CodeSystem"] ; # fhir:status [ fhir:v "draft"] ; # fhir:experimental [ fhir:v true] ; # fhir:date [ fhir:v "2026-03-13"^^xsd:date] ; # fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; # fhir:contact ( [ fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ; fhir:telecom ( [ fhir:system [ fhir:v "url" ] ; fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] [ fhir:system [ fhir:v "email" ] ; fhir:value [ fhir:v "clingenomics@lists.hl7.org" ] ] ) ] ) ; # fhir:description [ fhir:v "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."] ; # fhir:jurisdiction ( [ fhir:coding ( [ fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "001" ] ; fhir:display [ fhir:v "World" ] ] ) ] ) ; # fhir:caseSensitive [ fhir:v true] ; # fhir:valueSet [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-origin"^^xsd:anyURI ; fhir:l ] ; # fhir:content [ fhir:v "complete"] ; # fhir:concept ( [ fhir:code [ fhir:v "sequence-start" ] ; fhir:display [ fhir:v "Sequence Start" ] ; fhir:definition [ fhir:v "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)." ] ] [ fhir:code [ fhir:v "cds-start" ] ; fhir:display [ fhir:v "CDS Start (A of ATG)" ] ; fhir:definition [ fhir:v "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)." ] ] [ fhir:code [ fhir:v "feature-start" ] ; fhir:display [ fhir:v "Feature Start" ] ; fhir:definition [ fhir:v "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." ] ] [ fhir:code [ fhir:v "feature-end" ] ; fhir:display [ fhir:v "Feature End" ] ; fhir:definition [ fhir:v "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)." ] ] ) . # # -------------------------------------------------------------------------------------