genomic variation complement [GENO_0000009]

A genomic feature set representing all ‘variant single locus complements’ in a single genome, which together constitute the ‘variant’ component of a genomic genotype. A ‘complement’ refers to an exhaustive collection of all objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a ‘genomic variation complement’ is the set of all ‘single locus complements’ in a particular genome that harbor some known variation. In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one ‘single-locus variant complement’) that are variant realtive to some reference background. For example, the genotype instance ‘fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)).

Open genomic variation complement in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000009",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000009",
            "label": "genomic variation complement"
        },
        "description": [
            "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype."
        ],
        "comment": [
            "A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features.  Here, a 'genomic variation complement' is the set of all 'single locus complements' in a particular genome that harbor some known variation.\n\nIn model organisms, the majority of genotypes describe variation at a single  location in the genome (ie only one 'single-locus variant complement')  that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene))."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000660",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000660",
            "label": "genomic feature set"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/GENO_0000382",
                "label": "has_variant_part",
                "type": "has_variant_part"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/GENO_0000030",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "GENO_0000030",
                "label": "variant single locus complement"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}