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geno-base.json
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{
"graphs" : [ {
"id" : "http://purl.obolibrary.org/obo/geno/geno-base.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/elements/1.1/description",
"val" : "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"
}, {
"pred" : "http://purl.org/dc/elements/1.1/title",
"val" : "GENO ontology"
}, {
"pred" : "http://purl.org/dc/elements/1.1/type",
"val" : "http://purl.obolibrary.org/obo/IAO_8000001"
}, {
"pred" : "http://purl.org/dc/terms/license",
"val" : "https://creativecommons.org/licenses/by/4.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2023-10-08"
} ],
"version" : "http://purl.obolibrary.org/obo/geno/releases/2023-10-08/geno-base.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/GENO_0000484",
"lbl" : "exploratory term",
"type" : "INDIVIDUAL"
}, {
"id" : "http://purl.obolibrary.org/obo/IAO_0000102",
"lbl" : "data about an ontology part",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "ontology metadata"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000514",
"lbl" : "exemplar term",
"type" : "INDIVIDUAL"
}, {
"id" : "http://biohackathon.org/resource/faldo#BothStrandsPosition",
"lbl" : "Both strands",
"type" : "CLASS"
}, {
"id" : "http://biohackathon.org/resource/faldo#ExactPosition",
"lbl" : "Exact position",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A position that is exactly known."
}
}
}, {
"id" : "http://biohackathon.org/resource/faldo#ForwardStrandPosition",
"lbl" : "Positive strand",
"type" : "CLASS"
}, {
"id" : "http://biohackathon.org/resource/faldo#Position",
"lbl" : "Position",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "We place the FALDO:Position class under GENO:genomic location, as it represents a type of genomic location with an extent of 1 (i.e.has the same start and end coordinates - representing a single position as opposed to a location spanning a longer region)."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000412",
"val" : "FALDO"
} ]
}
}, {
"id" : "http://biohackathon.org/resource/faldo#Region",
"lbl" : "Region",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A region describes a length of sequence with a start position and end position that represents a feature on a sequence, e.g. a gene."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "From what I can tell, feature instances in data whose position is to be defined using FALDO are always mapped to a Region, and then the position of this Region is defined according to its location within some larger reference sequence. The exception may be feature instances that are explicitly part of the reference sequence on which its location is being defined (such that no 'mapping' to a reference is required). This suggests that, conceptually, we can think of a FALDO:Region as a subregion of a reference sequence that is mapped to from a feature of interest, in order to define its position with respect to that reference sequence."
} ]
}
}, {
"id" : "http://biohackathon.org/resource/faldo#ReverseStrandPosition",
"lbl" : "Negative strand",
"type" : "CLASS"
}, {
"id" : "http://biohackathon.org/resource/faldo#StrandedPosition",
"lbl" : "Stranded position",
"type" : "CLASS",
"meta" : {
"comments" : [ "Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'." ]
}
}, {
"id" : "http://biohackathon.org/resource/faldo#begin",
"lbl" : "begin",
"type" : "PROPERTY"
}, {
"id" : "http://biohackathon.org/resource/faldo#end",
"lbl" : "end",
"type" : "PROPERTY"
}, {
"id" : "http://biohackathon.org/resource/faldo#location",
"lbl" : "location",
"type" : "PROPERTY"
}, {
"id" : "http://biohackathon.org/resource/faldo#position",
"lbl" : "position",
"type" : "PROPERTY",
"meta" : {
"comments" : [ "The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is." ]
}
}, {
"id" : "http://biohackathon.org/resource/faldo#reference",
"lbl" : "reference (faldo)",
"type" : "PROPERTY",
"meta" : {
"definition" : {
"val" : "The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000001",
"lbl" : "entity",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "Julius Caesar"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "Verdi’s Requiem"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the Second World War"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "your body mass index"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000002",
"lbl" : "continuant",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000003",
"lbl" : "occurrent",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000004",
"lbl" : "independent continuant",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a chair"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a heart"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a leg"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a molecule"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a spatial region"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an atom"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an orchestra."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an organism"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the bottom right portion of a human torso"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the interior of your mouth"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000015",
"lbl" : "process",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a process of cell-division, \\ a beating of the heart"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a process of meiosis"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a process of sleeping"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the course of a disease"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the flight of a bird"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the life of an organism"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "your process of aging."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000016",
"lbl" : "disposition",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an atom of element X has the disposition to decay to an atom of element Y"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "certain people have a predisposition to colon cancer"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "children are innately disposed to categorize objects in certain ways."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the cell wall is disposed to filter chemicals in endocitosis and exocitosis"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000017",
"lbl" : "realizable entity",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the disposition of this piece of metal to conduct electricity."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the disposition of your blood to coagulate"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the function of your reproductive organs"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of being a doctor"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of this boundary to delineate where Utah and Colorado meet"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000019",
"lbl" : "quality",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the ambient temperature of this portion of air"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the color of a tomato"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the length of the circumference of your waist"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the mass of this piece of gold."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the shape of your nose"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the shape of your nostril"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000020",
"lbl" : "specifically dependent continuant",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "of one-sided specifically dependent continuants: the mass of this tomato"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the disposition of this fish to decay"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the function of this heart: to pump blood"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the pink color of a medium rare piece of grilled filet mignon at its center"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of being a doctor"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the shape of this hole."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the smell of this portion of mozzarella"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000023",
"lbl" : "role",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the priest role"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of a boundary to demarcate two neighboring administrative territories"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of a building in serving as a military target"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of a stone in marking a property boundary"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the role of subject in a clinical trial"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the student role"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "b is a role means: b is a realizable entity and b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be and b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000031",
"lbl" : "generically dependent continuant",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000040",
"lbl" : "material entity",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a flame"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a forest fire"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a human being"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a hurricane"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a photon"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a puff of smoke"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a sea wave"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "a tornado"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an aggregate of human beings."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an energy wave"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "an epidemic"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "the undetached arm of a human being"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000600",
"val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"
}, {
"pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy",
"val" : "http://purl.obolibrary.org/obo/bfo.owl"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000050",
"lbl" : "is part of",
"type" : "PROPERTY"
}, {
"id" : "http://purl.obolibrary.org/obo/BFO_0000051",
"lbl" : "has part",
"type" : "PROPERTY"
}, {
"id" : "http://purl.obolibrary.org/obo/CHEBI_23367",
"lbl" : "molecular entity",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/CHEBI_33696",
"lbl" : "nucleic acid",
"type" : "CLASS"
}, {
"id" : "http://purl.obolibrary.org/obo/CLO_0000031",
"lbl" : "cell line",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture)."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/CL_0000000",
"lbl" : "cell",
"type" : "CLASS",
"meta" : {
"comments" : [ "Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/ENVO_01000254",
"lbl" : "environmental system",
"type" : "CLASS",
"meta" : {
"comments" : [ "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions.\n\n2. Need to consdier how to model environments in a way that covers ENVO and XCO content in a consistent and coherent way. A couple classes under Exploratory Class are relvant here. Consider how we might approach environments/condisitons using an EQ aproach analogous to how phenotypes are defined (i.e. consider environments/coonditions as qualities inhereing in some entity)."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000000",
"lbl" : "genomic genotype (sex-agnostic)",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement)"
},
"comments" : [ "In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances)." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "Example zebrafish intrinsic genotype:\n\nGenotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB)\nreference component (genomic background) = AB \nvariant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392>\n\n. . . and within this variant component, there are two 'variant single locus complements' represented:\n\nallele complement 1 = fgf8a<ti282a/+>\nallele complement 2 = shha<tb392/tb392>\n\nand within each of these 'variant single locus complements' there is one or more variant gene locus member:\n\nin complement 1: fgf8a<ti282a>\nin complement 2: shha<ttb392>"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI).\n\nConceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "genotype"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "organismal genotype"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "sex-agnostic intrinsic genotype"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000002",
"lbl" : "variant allele",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location."
},
"comments" : [ "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "The use of the descriptor 'variant' here is consistent with naming recommendations from the ACMG Guidelines paper here: PMID:25741868. Generally, the descriptive labels chosen for subtypes of variant allele conform these recommendations as well, where 'variant' is used to cover mutant and polymorphic alleles."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "alternate allele"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "sequence-variant feature"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "variant feature"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000009",
"lbl" : "genomic variation complement",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype."
},
"comments" : [ "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))." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Note that even a reference feature (e.g. a wild-type gene) that is a member of a single locus complement that contains a variant allele is included in this 'genomic variation complement'. Thus, the members of this 'genomic variation complement' (which is a sequence collection) are 'single locus variant complements'. Our axiom below uses has_part rather than has_member, however, to account for the fact that many 'genomic variation complements' have only one 'single locus variant complement' as members. So because has_member is not reflexive, it is not appropriate for these cases."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000010",
"lbl" : "background genome",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)."
},
"xrefs" : [ {
"val" : "OBI:genetic population background information"
} ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Here, a 'genomic background' would differ form a 'reference genome' in that 'background' implies a derivation of the variant from the background (which is the case for most MOD strains), whereas a reference is simply meant as a target for comparison. But in a sense all background genomes are by default reference, in that the derived variant genome is compared against it."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "genomic background"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000014",
"lbl" : "gene allele",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A genomic feature that represents one of a set of versions of a gene (i.e. a haplotype whose extent is that of a gene)"
},
"comments" : [ "In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion.\n\nA genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene." ],
"xrefs" : [ {
"val" : "http://purl.obolibrary.org/obo/SO_0001023 ! allele"
} ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "The reference/wild-type cd99l2 danio rerio gene allele spans bases 27,004,426-27,021,059 on Chromosome 7. The \"mn004Gt\" represents an experimentally-created allele of this gene, in which sequence from a gene trap construct containing an RFP marker has been inserted at the cd99l2 gene locus. The resulting gene allele includes sequence from this construct that make it longer than the reference gene sequence, and also alter its seqauence in a way that prevents it from producing a functional product. The sequence extent of this cd99l2 gene allele is determined based on how its sequence aligns with that of the canonical gene and surrounding sequence in a reference genome.\n\nhttp://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722\n\nhttp://zfin.org/action/feature/feature-detail?zdbID=ZDB-ALT-111117-8"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Regarding the distinction between a 'gene' and a 'gene allele': Every zebrafish genome contains a 'gene allele' for every zebrafish gene. Many will be 'wild-type' or at least functional gene alleles. But some may be alleles that are mutated or truncated so as to lack functionality. According to current SO criteria defining genes, a 'gene' no longer exists in the case of a non-functional or deleted variant. But the 'gene allele' does exist - and its extent is that of the remaining/altered sequence based on alignment with a reference gene. Even for completely deleted genes, an allele of the gene exists (and here is equivalent to the junction corresponding to the where gene would live based on a reference alignment).\n\nThis design allows us to classify genes and any variants of those genes (be they functional or not) as the same type of thing (ie a 'gene allele'), since classification is based on genomic position rather than functional capacity. This is practical for representation of variant genotypes which often carry non-functional versions of a gene at a particular locus. What is important here is specifying what is present at a locus associated with a particular gene, whether or not it is a functional gene or not."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000017",
"lbl" : "reference sequence",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A sequence that serves as a standard against which other sequences at the same location are compared."
},
"comments" : [ "A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "The notion of a 'reference' in GENO is implemented at the level of 'biological sequence' rather than at the level of a sequence feature - i.e. we define a class for 'reference sequence' rather than reference sequence feature'. This is because it is at the *sequence* level that features of interest are determined to be variant or not. It is taken for granted that the *location* of the feature of interest is the same as that of the reference sequence to which it is compared, becasue an alignment process establishing common location always precedes the sequence comparison that determines if the feature is variant."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "reference sequence"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000019",
"lbl" : "obsolete sequence feature collection",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "a collection more than one sequence features (ie a collection of discontinuous sequence features)"
},
"comments" : [ "1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions." ],
"xrefs" : [ {
"val" : "perhaps not same as SO:sequence collection, as here we explicitly include features that can have an extent of zero (and SO:sequence collection is a collection of regions that have an extent of at least one)"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000022",
"lbl" : "obsolete genomic feature collection",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A sequence feature collection comprised of discontiguous sequences from a single genome"
},
"comments" : [ "Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Previously called 'genetic locus collection'. Difference between 'genetic' and 'genomic', as used here, is that 'genomic' implies a feature is a heritable part of some genome, while 'genetic' implies that it is part of some feature that is capable of contributing to gene expression in a cell or other biological system."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "genomic feature collection"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000029",
"lbl" : "obsolete reference single locus complement",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A single locus complement that serves as a standard against which 'variant' sequences are compared"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "reference allelic complement"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "reference single locus feature complement"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
"val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'single locus complement'\n and (has_sequence_attribute some reference)\n\nSC axioms:\n'has member' exactly 0 'variant allele'\n'has member' only 'reference genomic feature'\n'has member' some 'reference genomic feature'"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000030",
"lbl" : "variant single locus complement",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A single locus complement in which at least one member allele is considered variant, and/or the total number of features in the complement deviates from the normal poloidy of the reference genome (e.g. trisomy 13)."
},
"comments" : [ "Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members.\n\nNote that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "variant allelic complement"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000033",
"lbl" : "variant genome",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A genome that varies at one or more loci from the sequence of some reference genome."
},
"xrefs" : [ {
"val" : "http://purl.obolibrary.org/obo/SO_0001506 ! variant_genome (definition of SO term here is too vague to know if has same meaning as GENO class here)"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000036",
"lbl" : "reference allele",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome."
},
"comments" : [ "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000037",
"lbl" : "obsolete unspecified feature",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)."
},
"comments" : [ "An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele)." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/GENO_0000484"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Uses as a term of convenience for describing data reporting unspecified alleles in a genotype (i.e. in cases where zygosoty for a given locus is not known). Typlically recorded in genotype syntaxes as a ' /? '."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
"val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class def: 'genomic feature'\n and (has_sequence_attribute some unspecified)"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000042",
"lbl" : "obsolete reference junction",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A junction found at a chromosomal position where an insertion has occurred on the homologous chromosome, such that the junction represents the reference feature paired with the hemizygously inserted feature."
},
"comments" : [ "In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction.\n\nThe junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "hemizygous reference junction"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
"val" : "Eliminating unecessary defined/organizational classes. Former logical def:\n\njunction\n and (has_sequence_attribute some reference)\n\nSubclass axiom:\nis_variant_with some insertion"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000047",
"lbl" : "danio rerio gene",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A gene that originates from the genome of a danio rerio."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000054",
"lbl" : "homo sapiens gene",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A gene that originates from the genome of a homo sapiens."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000057",
"lbl" : "mus musculus gene",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A gene that originates from the genome of a mus musculus."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000060",
"lbl" : "obsolete reference gene allele",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A version/allele of a gene that serves as a standard against which variant genes are compared."
},
"comments" : [ "Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene.\n\nIn model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
"val" : "A reference human sonic hedgehog (shh) gene spans bases 155,592,680-155,604,967 on Chromosome 7, according to genome build GRCh37, and produces a primary funcitonal transcript that is 4454 bp in length and produces a 462 amino acid protein involved in cell signaling events behind various aspects of cell differentiation and development.\nhttp://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690\n\nNote that this may be slightly different than the extend described in other gene databases, such as Entrez Gene:http://www.ncbi.nlm.nih.gov/gene/6469"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "reference gene"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
"val" : "Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity.\n\nEq Class axiom:\n'gene allele'\n and (has_sequence_attribute some reference)\n\nSC axioms:\nis_variant_with some 'gene allele'\nis_reference_allele_of some gene"
} ],
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000091",
"lbl" : "obsolete experimental insertion",
"type" : "CLASS",
"meta" : {
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000092",
"lbl" : "gene trap insertion",
"type" : "CLASS"
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000093",
"lbl" : "integrated transgene",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A transgene that has been integrated into a chrromosome in the host genome."
},
"comments" : [ "An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion.\n\nAn 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome." ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000106",
"lbl" : "genomic material",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A nucleic acid macromolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or is capable of being replicated and inherited through successive generations of progeny."
},
"comments" : [ "1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
"val" : "http://purl.obolibrary.org/obo/GENO_0000484"
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "1. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genomic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome.\n\n2. A challenging edge case is experimentally delivered DNA into a terminally differentiated cell that will never divide. Such material does technically meet our definition - since we are careful to say that the material must be *capable of* being stably inherited through subsequent generations. Thus, we would say that *if* the cell were resume replication, the material would be heritable in this way."
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000108",
"lbl" : "material genome",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion."
},
"comments" : [ "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements.\n\nNote that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome." ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "physical genome"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000111",
"lbl" : "human population",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)"
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")."
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "homo sapiens population"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000112",
"lbl" : "strain or breed",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical."
},
"comments" : [ "Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)" ],
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
"val" : "organism strain or breed"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000113",
"lbl" : "taxonomic group",
"type" : "CLASS",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
"val" : "A group comprised of organisms from a single taxonomic group (e.g. family, order, genus, species, or a strain or breed within a given taxon)"
} ]
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000118",
"lbl" : "mus musculus strain",
"type" : "CLASS"
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000119",
"lbl" : "danio rerio strain",
"type" : "CLASS"
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000125",
"lbl" : "obsolete sequence feature collection attribute",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "sequence attribute that can inhere only in a collection of more than one sequence features"
},
"deprecated" : true
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000131",
"lbl" : "in cis",
"type" : "CLASS",
"meta" : {
"definition" : {
"val" : "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes)."
}
}
}, {
"id" : "http://purl.obolibrary.org/obo/GENO_0000132",