Preferred Label : Genomic coordinate system:Type:Pt:XXX:Nom:Molgen;
LOINC status : ACTIVE;
LOINC display name : Genomic coordinate system Molgen Nom (Specimen);
LOINC long common name : Genomic coordinate system [Type];
LOINC short name : Genomic coord system;
LOINC 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.;
Origin ID : 92822-6;
UMLS CUI : C5144711;
Has component
- Has method
- Has property
- Has scale
- Has system
- Has time aspect
- Semantic type(s)
