genomic feature location [GENO_0000902]

The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a ‘sequence feature’ - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the ‘ATG’ sequence beginning the ORF of the human SHH gene shares the same sequence as the ‘ATG’ beginning the ORF of the human AKT gene. But these are distinct sequence features because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.

Open genomic feature location in VFB

VFB Term Json

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            "iri": "http://purl.obolibrary.org/obo/GENO_0000902",
            "symbol": "",
            "types": [
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            "short_form": "GENO_0000902",
            "label": "genomic feature location"
        },
        "description": [
            "The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system"
        ],
        "comment": [
            "1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there.  In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies).  For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. \n\t\n2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene).  And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus.\n\n3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it.  As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
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            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000815",
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                "Class"
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            "short_form": "GENO_0000815",
            "label": "sequence feature location"
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