genomic feature set [GENO_0000660]

A set of genomic features (i.e. sequence features that are of genomic origin). A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. ‘Sets’ are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an ’empty’ set) or 1 member (a ‘singleton’ or ‘unit’ set), consistent with the concept of ‘mathematical sets’. For example, a ‘single locus complement’ at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous ‘single locus complement’ is a set comprised of two of the same feature. The notion of a ‘genomic feature set’ differs from that of a ‘genomic sequence set’ in that we are counting how many copies of the same sequence feature exist in a genome, as opposed to how many of the same sequence. ‘Genomic feature sets are useful for representing things like ‘single locus complements’, where members are sequence features whose identity is dependent on their location. By contrast, ‘genomic sequence sets’ are useful for describing things like ‘copy number complements’, which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.

Open genomic feature set in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000660",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000660",
            "label": "genomic feature set"
        },
        "description": [
            "A set of genomic features (i.e. sequence features that are of genomic origin)."
        ],
        "comment": [
            "A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature.\n\nThe notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000897",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000897",
            "label": "genomic entity"
        },
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000659",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000659",
            "label": "sequence feature set"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/RO_0002351",
                "label": "has_member",
                "type": "has_member"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/GENO_0000481",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "GENO_0000481",
                "label": "genomic feature"
            }
        }
    ],
    "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": ""
        }
    ]
}