Genotype Ontology

Last uploaded: June 25, 2019
Preferred Name

allele

Definitions

An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence). One of a set of sequence features known to exist at a particular genomic location.

ID

http://purl.obolibrary.org/obo/GENO_0000512

comment

An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).

alternative term

variable feature

definition

One of a set of sequence features known to exist at a particular genomic location.

editor note

A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. [1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) [2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) [3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) [4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) [5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) [6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) [6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 [7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) [8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) [9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) [10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) [11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)

label

allele

prefixIRI

GENO:0000512

prefLabel

allele

subClassOf

http://purl.obolibrary.org/obo/GENO_0000481

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http://purl.jp/bio/4/id/200906060354973560 IOBC LOOM
http://semanticscience.org/resource/Allele CHEAR LOOM
http://semanticscience.org/resource/Allele HASCO LOOM
http://purl.org/stemnet/MHC#Allele MHC LOOM
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Allele CSEO LOOM
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Allele MO LOOM
http://bioportal/bioontology.org/ontologies/HIVO0004#OWLClass_7d387a65_275c_4773_968d_2001fff0b50c HIVO004 LOOM
http://www.w3.org/2001/sw/hcls/ns/transmed/TMO_0048 TMO LOOM
http://purl.obolibrary.org/obo/ODGI.owl#Allele OGDI LOOM
http://purl.phyloviz.net/ontology/typon#Allele TYPON LOOM
http://purl.obolibrary.org/obo/SO_0001023 SO LOOM
http://purl.obolibrary.org/obo/SO_0001023 ORTH LOOM
http://purl.obolibrary.org/obo/SO_0001023 NIFSTD LOOM
http://www.projecthalo.com/aura#Allele AURA LOOM
http://www.imgt.org/download/IMGT-ONTOLOGY/IMGT-ONTOLOGY-v1-0-3.owl#Allele IMGT-ONTOLOGY LOOM
http://sbmi.uth.tmc.edu/ontology/ochv#C0002085 OCHV LOOM
http://semanticscience.org/resource/SIO_010277 ORTH LOOM
http://semanticscience.org/resource/SIO_010277 BIOMO LOOM
http://semanticscience.org/resource/SIO_010277 SIO LOOM
http://www.genomic-cds.org/ont/genomic-cds.owl#allele GENE-CDS LOOM
http://purl.obolibrary.org/obo/OGI_0000008 OGSF LOOM
http://purl.obolibrary.org/obo/OGI_0000008 OGI LOOM
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16277 NCIT LOOM
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16277 NCIT LOOM
http://purl.org/obo/owl/SO#SO_0001203 ONSTR LOOM
http://purl.bioontology.org/ontology/CSP/1256-6342 CRISP LOOM