Version 2.77

Term Description

A genomic coordinate is a position along a sequence. Coordinate systems can start counting from:

0-based interval counting
- Used by: GA4GH API, ClinGen data model, BED & BAM files, UCSC files, HLM 1.0 and NCBI's SPDI conversion format
- Akin to cursor positioning in modern text editors with cursor between characters
- A bit unnatural for humans, easier for computers
- Sequences have an inclusive start and exclusive end
- Insertions always go in the interval between characters

0-based character counting
- Used by: Genbank database & ASN files
- Sequences have an inclusive start, exclusive end
- Length = end - start
- A bit unnatural for human reading, easier for computers
- Sequences have an inclusive start and inclusive end
- Insertions not defined because GenBank and ASN do not model insertions to records they contain (historically ASN did internal to NCBI). SPDI was developed in part because of this inability to model insertions.

1-based character counting
- Used by: HGVS, VCF, NCBI's ClinVar (uses HGVS), Genbank files, IPD-IMGT/HLA, UCSC genome browser (note different from UCSC file, which uses 0-based interval counting)
- Akin to approach used in the earliest text processors
- Length = (end - start) + 1
- Sequences have inclusive start and inclusive end
- More natural for humans
- Insertions. Be careful in theory for 1-base, the insertion location could be defined in three ways: a) before position, b) after position, c) specify the di-nucleotide which where the insertion goes; but in practice there is only one way to do it per coordinate type.

Distinctions for describing sub sequences with the three approaches with examples
Consider ACGTAGTC as an example string and what nucleotides would be in the range 2-4
- 0-based interval counting (e.g..SPDI): GT
- 0-based character counting (i.e. GenBank): GTA
- 1-based character counting (i.e. VCF): CGT

Distinctions regarding insertions with examples. Insertions can be tricky with character counting.
Now consider that you want to describe an insertion between T&A (4th and 5th characters in the example string):
- 0-based interval counting (i.e. SPDI) insert at position 4.
- 0-based character counting. Insert between 3&4. Note: insertions are not supported in GenBank's model.
- 1-based character counting. Insert between 4&5. Note: HGVS requires specification of the dinucleotide between which the insertion goes. For VCF, this would be represented as insert after 4 and does not require other information but the result is the same.
Source: Regenstrief LOINC

Fully-Specified Name

Component
Genomic coordinate system
Property
Type
Time
Pt
System
XXX
Scale
Nom
Method
Molgen

Additional Names

Short Name
Genomic coord system
Display Name
Genomic coordinate system Molgen Nom (Specimen)
Consumer Name Alpha Get Info
Genomic coordinate system, Specimen

Preferred Answer List: LL5323-2

Source: National Library of Medicine
Answer Code Score Answer ID
0-based interval counting LA30100-4
0-based character counting LA30101-2
1-based character counting LA30102-0

Basic Attributes

Class
MOLPATH
Type
Laboratory
First Released
Version 2.66
Last Updated
Version 2.72
Order vs. Observation
Observation

Language Variants Get Info

Tag Language Translation
es-ES Spanish (Spain) Sistema de coordenadas genómicas:Tipo:Punto temporal:XXX:Nom:Genética molecular
es-MX Spanish (Mexico) Sistema de coordenadas genómicas:Tipo:Punto temporal:XXX:Nominal:Genética molecular
fr-FR French (France) System de coordination génomique:Type:Ponctuel:Milieux divers:Résultat nominal:Biologie moléculaire
it-IT Italian (Italy) Coordinate genomiche, sistema:Tipo:Pt:XXX:Nom:Molgen
Synonyms: Genetica molecolare Patologia molecolare Punto nel tempo (episodio) Sistema di coordinate genomiche
zh-CN Chinese (China) 基因组坐标系统:类型:时间点:XXX:名义型:分子遗传学类实验室方法
Synonyms: 不明的;其他;将在相应消息内其他部分之中加以详细说明;未作详细说明的;未作说明的;未做说明的标本;未加规定的;未加说明的标本;杂项 分子病理学;分子病理学试验 分子遗传学;分子遗传学方法;分子遗传学类方法;分子遗传学类检验方法;包括 RFL、PCR 及其他方法在内，用于在分子基础上检测遗传属性的方法的大类;聚合酶链反应;聚合酶链式反应 分类型应答;分类型结果;名义性;名称型;名词型;名词性;标称性;没有自然次序的名义型或分类型应答 型 基因组坐标系;基因组座标系统;基因组座标系;基因组坐标制;GCS 时刻;随机;随意;瞬间

LOINC Terminology Service (API) using HL7® FHIR® Get Info

CodeSystem lookup
https://fhir.loinc.org/CodeSystem/$lookup?system=http://loinc.org&code=92822-6