obsolete contextual allele [GENO_0000891]

An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence. The notion of a ‘contextual allele’ derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single ‘canonical allele’, which in turn may aggregate any number of ‘contextual allele’ representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.

Open obsolete contextual allele in VFB

Term Information

  • ID: GENO_0000891
  • Name: obsolete contextual allele
  • Definition: An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.
  • Synonyms:
  • Type:
  • Comment: The notion of a ‘contextual allele’ derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single ‘canonical allele’, which in turn may aggregate any number of ‘contextual allele’ representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000891",
            "symbol": "",
            "types": [
                "Entity",
                "Class",
                "Deprecated"
            ],
            "short_form": "GENO_0000891",
            "unique_facets": [
                "Deprecated"
            ],
            "label": "obsolete contextual allele"
        },
        "description": [
            "An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence."
        ],
        "comment": [
            "The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles \u201cNC_000013.11:g.32319070T>A\u201d and \u201cNG_012772.3:g.8591T>A\u201d both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene."
        ]
    },
    "query": "Get JSON for Class",
    "version": "c58c844",
    "parents": [],
    "relationships": [],
    "related_individuals": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "unique_facets": [
                    "pub"
                ],
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}