geno-base.obo

format-version: 1.2
data-version: geno/releases/2023-10-08/geno-base.owl
ontology: geno/geno-base
property_value: http://purl.org/dc/elements/1.1/description "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" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "GENO ontology" xsd:string
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/
property_value: owl:versionInfo "2023-10-08" xsd:string

[Term]
id: BFO:0000001
name: entity
property_value: IAO:0000112 "Julius Caesar" xsd:string
property_value: IAO:0000112 "the Second World War" xsd:string
property_value: IAO:0000112 "Verdi’s Requiem" xsd:string
property_value: IAO:0000112 "your body mass index" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000002
name: continuant
is_a: BFO:0000001 ! entity
disjoint_from: BFO:0000003 ! occurrent
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000003
name: occurrent
is_a: BFO:0000001 ! entity
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000004
name: independent continuant
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000112 "a chair" xsd:string
property_value: IAO:0000112 "a heart" xsd:string
property_value: IAO:0000112 "a leg" xsd:string
property_value: IAO:0000112 "a molecule" xsd:string
property_value: IAO:0000112 "a spatial region" xsd:string
property_value: IAO:0000112 "an atom" xsd:string
property_value: IAO:0000112 "an orchestra." xsd:string
property_value: IAO:0000112 "an organism" xsd:string
property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string
property_value: IAO:0000112 "the interior of your mouth" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000015
name: process
def: "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])" []
is_a: BFO:0000003 ! occurrent
property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string
property_value: IAO:0000112 "a process of meiosis" xsd:string
property_value: IAO:0000112 "a process of sleeping" xsd:string
property_value: IAO:0000112 "the course of a disease" xsd:string
property_value: IAO:0000112 "the flight of a bird" xsd:string
property_value: IAO:0000112 "the life of an organism" xsd:string
property_value: IAO:0000112 "your process of aging." xsd:string
property_value: IAO:0000116 "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)" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000016
name: disposition
is_a: BFO:0000017 ! realizable entity
disjoint_from: BFO:0000023 ! role
property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string
property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string
property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string
property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocitosis and exocitosis" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000017
name: realizable entity
is_a: BFO:0000020 ! specifically dependent continuant
disjoint_from: BFO:0000019 ! quality
property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string
property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string
property_value: IAO:0000112 "the function of your reproductive organs" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000019
name: quality
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string
property_value: IAO:0000112 "the color of a tomato" xsd:string
property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string
property_value: IAO:0000112 "the mass of this piece of gold." xsd:string
property_value: IAO:0000112 "the shape of your nose" xsd:string
property_value: IAO:0000112 "the shape of your nostril" xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000020
name: specifically dependent continuant
def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1  i < j  n, ci  and cj share no common parts, are such that for each 1  i  n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" []
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "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" xsd:string
property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string
property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string
property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string
property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string
property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string
property_value: IAO:0000112 "the role of being a doctor" xsd:string
property_value: IAO:0000112 "the shape of this hole." xsd:string
property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000023
name: role
is_a: BFO:0000017 ! realizable entity
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "the priest role" xsd:string
property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string
property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string
property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string
property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string
property_value: IAO:0000112 "the student role" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000031
name: generically dependent continuant
def: "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])" []
is_a: BFO:0000002 ! continuant
property_value: IAO:0000112 "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." xsd:string
property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string
property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BFO:0000040
name: material entity
is_a: BFO:0000004 ! independent continuant
property_value: IAO:0000112 "a flame" xsd:string
property_value: IAO:0000112 "a forest fire" xsd:string
property_value: IAO:0000112 "a human being" xsd:string
property_value: IAO:0000112 "a hurricane" xsd:string
property_value: IAO:0000112 "a photon" xsd:string
property_value: IAO:0000112 "a puff of smoke" xsd:string
property_value: IAO:0000112 "a sea wave" xsd:string
property_value: IAO:0000112 "a tornado" xsd:string
property_value: IAO:0000112 "an aggregate of human beings." xsd:string
property_value: IAO:0000112 "an energy wave" xsd:string
property_value: IAO:0000112 "an epidemic" xsd:string
property_value: IAO:0000112 "the undetached arm of a human being" xsd:string
property_value: IAO:0000116 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000600 "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])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Term]
id: BothStrandsPosition
name: Both strands
is_a: StrandedPosition ! Stranded position

[Term]
id: CHEBI:23367
name: molecular entity
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology." xsd:string

[Term]
id: CHEBI:33696
name: nucleic acid
is_a: CHEBI:23367 ! molecular entity

[Term]
id: CL:0000000
name: cell
comment: Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.
is_a: UBERON:0001062 ! anatomical entity

[Term]
id: CLO:0000031
name: cell line
def: "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)." []
is_a: BFO:0000040 ! material entity
relationship: RO:0001000 OBI:0100026 ! derives from organism

[Term]
id: ENVO:01000254
name: environmental system
comment: 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.
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "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)." xsd:string

[Term]
id: ExactPosition
name: Exact position
def: "A position that is exactly known." []
is_a: Position ! Position

[Term]
id: ForwardStrandPosition
name: Positive strand
is_a: StrandedPosition ! Stranded position

[Term]
id: GENO:0000000
name: genomic genotype (sex-agnostic)
def: "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)" []
comment: 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).
is_a: GENO:0000899 ! genomic genotype
property_value: IAO:0000112 "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>" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "genotype" xsd:string
property_value: IAO:0000118 "organismal genotype" xsd:string
property_value: IAO:0000118 "sex-agnostic intrinsic genotype" xsd:string

[Term]
id: GENO:0000002
name: variant allele
def: "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location." []
comment: 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.
intersection_of: GENO:0000512 ! allele
intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "alternate allele" xsd:string
property_value: IAO:0000118 "sequence-variant feature" xsd:string
property_value: IAO:0000118 "variant feature" xsd:string

[Term]
id: GENO:0000009
name: genomic variation complement
def: "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)).
intersection_of: GENO:0000660 ! genomic feature set
intersection_of: GENO:0000382 GENO:0000030 ! has_variant_part variant single locus complement
property_value: IAO:0000116 "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." xsd:string

[Term]
id: GENO:0000010
name: background genome
def: "A reference genome that represents the sequence of a genome from which a variant genome is derived  (through the introduction of sequence alterations)." []
xref: OBI:genetic population background information
is_a: GENO:0000914 ! reference genome
property_value: IAO:0000112 "The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)" xsd:string
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "genomic background" xsd:string

[Term]
id: GENO:0000014
name: gene allele
def: "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)" []
comment: 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.
xref: http://purl.obolibrary.org/obo/SO_0001023 ! allele
is_a: GENO:0000512 ! allele
relationship: GENO:0000408 SO:0000704 ! is_allele_of gene
property_value: IAO:0000112 "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" xsd:string
property_value: IAO:0000116 "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." xsd:string

[Term]
id: GENO:0000017
name: reference sequence
def: "A sequence that serves as a standard against which other sequences at the same location are compared." []
comment: 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.
intersection_of: GENO:0000702 ! biological sequence
intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "reference sequence" xsd:string

[Term]
id: GENO:0000019
name: obsolete sequence feature collection
def: "a collection more than one sequence features (ie a collection of discontinuous sequence features)" []
comment: 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.
xref: 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)
is_obsolete: true

[Term]
id: GENO:0000022
name: obsolete genomic feature collection
def: "A sequence feature collection comprised of discontiguous sequences from a single genome" []
comment: 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.
property_value: IAO:0000116 "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." xsd:string
property_value: IAO:0000118 "genomic feature collection" xsd:string
is_obsolete: true

[Term]
id: GENO:0000029
name: obsolete reference single locus complement
def: "A single locus complement that serves as a standard against which 'variant' sequences are compared" []
property_value: IAO:0000118 "reference allelic complement" xsd:string
property_value: IAO:0000118 "reference single locus feature complement" xsd:string
property_value: IAO:0000231 "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'" xsd:string
is_obsolete: true

[Term]
id: GENO:0000030
name: variant single locus complement
def: "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)." []
comment: 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.
intersection_of: GENO:0000516 ! single locus complement
intersection_of: GENO:0000382 GENO:0000002 ! has_variant_part variant allele
property_value: IAO:0000118 "variant allelic complement" xsd:string

[Term]
id: GENO:0000033
name: variant genome
def: "A genome that varies at one or more loci from the sequence of some reference genome." []
xref: 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)
intersection_of: SO:0001026 ! genome
intersection_of: GENO:0000683 GENO:0000914 ! varies_with reference genome
relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration

[Term]
id: GENO:0000036
name: reference allele
def: "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome." []
comment: 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.
intersection_of: GENO:0000512 ! allele
intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference

[Term]
id: GENO:0000037
name: obsolete unspecified feature
def: "A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus)." []
comment: 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).
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "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 ' /? '." xsd:string
property_value: IAO:0000231 "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)" xsd:string
is_obsolete: true

[Term]
id: GENO:0000042
name: obsolete reference junction
def: "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." []
comment: 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.
property_value: IAO:0000118 "hemizygous reference junction" xsd:string
property_value: IAO:0000231 "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" xsd:string
is_obsolete: true

[Term]
id: GENO:0000047
name: danio rerio gene
def: "A gene that originates from the genome of a danio rerio." []
intersection_of: SO:0000704 ! gene
intersection_of: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio

[Term]
id: GENO:0000054
name: homo sapiens gene
def: "A gene that originates from the genome of a homo sapiens." []
intersection_of: SO:0000704 ! gene
intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens

[Term]
id: GENO:0000057
name: mus musculus gene
def: "A gene that originates from the genome of a mus musculus." []
intersection_of: SO:0000704 ! gene
intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus

[Term]
id: GENO:0000060
name: obsolete reference gene allele
def: "A version/allele of a gene that serves as a standard against which variant genes are compared." []
comment: 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.
property_value: IAO:0000112 "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" xsd:string
property_value: IAO:0000118 "reference gene" xsd:string
property_value: IAO:0000231 "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" xsd:string
is_obsolete: true

[Term]
id: GENO:0000091
name: obsolete experimental insertion
is_obsolete: true

[Term]
id: GENO:0000092
name: gene trap insertion
is_a: SO:0000667 ! insertion

[Term]
id: GENO:0000093
name: integrated transgene
def: "A transgene that has been integrated into a chrromosome in the host genome." []
comment: 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.
is_a: SO:0000902 ! transgene
relationship: BFO:0000050 SO:0001218 ! is part of transgenic_insertion

[Term]
id: GENO:0000106
name: genomic material
def: "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." []
comment: 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.
is_a: GENO:0000482 ! genetic material
relationship: RO:0000091 GENO:0000139 ! has disposition heritable
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "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." xsd:string

[Term]
id: GENO:0000108
name: material genome
def: "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." []
comment: 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.
is_a: BFO:0000040 ! material entity
property_value: IAO:0000118 "physical genome" xsd:string

[Term]
id: GENO:0000111
name: human population
def: "a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)" []
is_a: OBI:0000181 ! population
property_value: IAO:0000116 "Consider http://semanticscience.org/resource/SIO_001062 ! human population (\"A human population refers to a collection of human beings\")." xsd:string
property_value: IAO:0000118 "homo sapiens population" xsd:string

[Term]
id: GENO:0000112
name: strain or breed
def: "A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical." []
comment: Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)
is_a: GENO:0000113 ! taxonomic group
relationship: RO:0002162 OBI:0100026 ! in taxon organism
property_value: IAO:0000118 "organism strain or breed" xsd:string

[Term]
id: GENO:0000113
name: taxonomic group
is_a: PCO:0000000 ! collection of organisms
property_value: IAO:0000116 "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)" xsd:string

[Term]
id: GENO:0000118
name: mus musculus strain
is_a: GENO:0000112 ! strain or breed

[Term]
id: GENO:0000119
name: danio rerio strain
is_a: GENO:0000112 ! strain or breed
relationship: RO:0002351 NCBITaxon:7955 {all_only="true"} ! has member Danio rerio
relationship: RO:0002351 NCBITaxon:7955 ! has member Danio rerio

[Term]
id: GENO:0000125
name: obsolete sequence feature collection attribute
def: "sequence attribute that can inhere only in a collection of more than one sequence features" []
is_obsolete: true

[Term]
id: GENO:0000131
name: in cis
def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes)." []
is_a: GENO:0000886 ! allelic phase

[Term]
id: GENO:0000132
name: in trans
def: "A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes)." []
is_a: GENO:0000886 ! allelic phase

[Term]
id: GENO:0000133
name: zygosity
def: "An allelic state that describes the degree of similarity between features in a 'single locus complement', within the genome of a cell or organism (i.e., whether the alleles or haplotypes that reside at the same location on paired chromosomes are the same or different)." []
xref: http://semanticscience.org/resource/SIO_001263
is_a: GENO:0000875 ! allelic state
relationship: RO:0000052 GENO:0000516 ! inheres_in single locus complement
property_value: IAO:0000118 "allelic state" xsd:string
property_value: IAO:0000119 "derived from https://en.wikipedia.org/wiki/Zygosity" xsd:string

[Term]
id: GENO:0000134
name: hemizygous
def: "A zygosity quality inhering in a 'single locus complement' with half the number of alleles than normal (e.g. a single allele in a diploid genome, for example, a locus on the Y chromosome in a eukaryotic male genome, or a transgene that is present only in one of the two parental chromosome sets)" []
is_a: GENO:0000391 ! disomic zygosity

[Term]
id: GENO:0000135
name: heterozygous
def: "A zygosity quality inhering in a 'single locus complement' where the copies of the feature at this location have at least one difference in sequence  (in a eukaryotic diploid genome, this means having two distinct alleles on each of the two homologous chromosomes, one inherited from each parent)." []
is_a: GENO:0000391 ! disomic zygosity

[Term]
id: GENO:0000136
name: homozygous
def: "A zygosity quality inhering in a 'single locus complement' where all copies of the feature at this location have the same sequence (in a eukaryotic diploid genome, this means having identical alleles on each of the two homologous chromosomes, one inherited from each parent)." []
is_a: GENO:0000391 ! disomic zygosity

[Term]
id: GENO:0000137
name: unspecified zygosity
is_a: GENO:0000133 ! zygosity
property_value: IAO:0000118 "indeterminite zygosity" xsd:string {comment="MGI uses this term when zygosity is not known."}
property_value: IAO:0000118 "no-call zygosity" xsd:string {comment="(this is how the GVF10 format/standard refers to loci without enough data to make an accurate call . . . see http://www.sequenceontology.org/resources/gvf.html#quick_gvf_examples)"}
property_value: IAO:0000118 "unknown zygosity" xsd:string

[Term]
id: GENO:0000138
name: heritabililty
def: "The disposition of an entity to be transmitted to subsequent generations following a genetic replication or organismal reproduction event." []
comment: We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms).  Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells).\n\nWe can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms.
is_a: BFO:0000016 ! disposition

[Term]
id: GENO:0000139
name: heritable
is_a: GENO:0000138 ! heritabililty

[Term]
id: GENO:0000140
name: non-heritable
is_a: GENO:0000138 ! heritabililty

[Term]
id: GENO:0000141
name: inheritance pattern
def: "The pattern in which a genetic trait or condition is passed from one generation to the next, as determined by genetic interactions between alleles of the causal gene, and interactions between these alleles and the environment." []
comment: An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context.  Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. \n\nThese genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y.
xref: http://purl.obolibrary.org/obo/HP_0000005
xref: http://purl.obolibrary.org/obo/NCIT_C45827
is_a: BFO:0000016 ! disposition
property_value: IAO:0000116 "The subtypes of inheritance pattern in this hierarchy are largely distinguished based on the underlying genetic mechanism, which will manifest in a characteristic pattern of traits in affected and unaffected family members. For example, 'autosomal dominant inheritance' defines an inheritance pattern that is caused by the interaction of alleles on non-sex chromosomes wherein the trait manifests even in heterozygotes - resulting in a characteristic pattern of 'dominant' inheritance across generations of individuals in a family." xsd:string
property_value: IAO:0000118 "mode of inheritance" xsd:string
property_value: IAO:0000118 "phenotypic inheritance pattern" xsd:string

[Term]
id: GENO:0000142
name: obsolete dominant inheritance
def: "disposition inhering in a genetic locus variant that is realized in its inheritance by some offspring such that at least a partial variant-associated phenotype is apparent in heterozygotes" []
property_value: IAO:0000231 "Triage until decide if want to define this as grouping class that would result in multiple-inheritance." xsd:string
is_obsolete: true

[Term]
id: GENO:0000143
name: co-dominant autosomal inheritance
def: "An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." []
is_a: GENO:0000147 ! autosomal dominant inheritance

[Term]
id: GENO:0000144
name: complete autosomal dominant inheritance
def: "An autosomal dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." []
is_a: GENO:0000147 ! autosomal dominant inheritance
property_value: IAO:0000118 "pure dominant inheritance" xsd:string

[Term]
id: GENO:0000145
name: incomplete autosomal dominant inheritance
def: "An autosomal dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." []
is_a: GENO:0000147 ! autosomal dominant inheritance
property_value: IAO:0000118 "intermediate dominant autosomal inheritance" xsd:string
property_value: IAO:0000118 "semi-dominant autosomal inheritance" xsd:string

[Term]
id: GENO:0000146
name: X-linked dominant inheritance
def: "An X-linked inheritance pattern wherein the trait manifests in heterozygotes." []
xref: http://purl.obolibrary.org/obo/HP_0001423
is_a: GENO:0000936 ! X-linked inheritance

[Term]
id: GENO:0000147
name: autosomal dominant inheritance
def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes." []
xref: http://purl.obolibrary.org/obo/HP_0000006
is_a: GENO:0000934 ! autosomal inheritance
property_value: IAO:0000118 "vertical inheritance" xsd:string

[Term]
id: GENO:0000148
name: autosomal recessive inheritance
def: "An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals." []
is_a: GENO:0000934 ! autosomal inheritance

[Term]
id: GENO:0000149
name: X-linked recessive inheritance
def: "An X-linked inheritance pattern wherein a trait caused by alleles of a gene on the X-chromosome manifests in homozygous but not heterozygote individuals." []
xref: http://purl.obolibrary.org/obo/HP_0001419
is_a: GENO:0000936 ! X-linked inheritance

[Term]
id: GENO:0000150
name: obsolete autosomal recessive inheritance
property_value: IAO:0000231 "duplicate term, use GENO:0000148" xsd:string
is_obsolete: true

[Term]
id: GENO:0000152
name: reference
def: "An attribute inhering in a feature that is designated to serve as a standard against which 'variant' versions of the same location are compared." []
comment: Being 'reference' is a role or status assigned in the context of a data set or analysis framework.  A given allele can be reference on one context and variant in another.
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000160
name: unspecified life cycle stage
is_a: UBERON:0000105 ! life cycle stage

[Term]
id: GENO:0000164
name: obsolete genetic insertion technique
is_obsolete: true

[Term]
id: GENO:0000165
name: obsolete mutagen treatment technique
is_obsolete: true

[Term]
id: GENO:0000166
name: obsolete targeted gene mutation technique
is_obsolete: true

[Term]
id: GENO:0000169
name: obsolete random genetic insertion technique
is_obsolete: true

[Term]
id: GENO:0000170
name: obsolete targeted genetic insertion technique
is_obsolete: true

[Term]
id: GENO:0000171
name: obsolete enhancer trapping technique
is_obsolete: true

[Term]
id: GENO:0000172
name: obsolete gene trapping technique
is_obsolete: true

[Term]
id: GENO:0000173
name: obsolete promoter trapping technique
is_obsolete: true

[Term]
id: GENO:0000174
name: obsolete targeted knock-in technique
is_obsolete: true

[Term]
id: GENO:0000175
name: obsolete random transgene insertion technique
is_obsolete: true

[Term]
id: GENO:0000324
name: obsolete chromosome complement
def: "A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome" []
is_obsolete: true

[Term]
id: GENO:0000338
name: gained aneusomic chromosome
def: "A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation" []
comment: This 'gained' chromosome is conceptually an 'insertion' in a genome  that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome.
is_a: GENO:0000346 ! aneusomic chromosome
relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000118 "duplicate chromosome" xsd:string

[Term]
id: GENO:0000339
name: lost aneusomic chromosome
def: "A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation." []
is_a: GENO:0000346 ! aneusomic chromosome
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "This 'lost' chromosome is conceptually a 'deletion' in a genome that received zero copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration. But it doesn't classify under SO:deletion because this class is defined as \"the point at which one or more contiguous nucleotides were excised\"." xsd:string
property_value: IAO:0000118 "absent aneusomic chromosome" xsd:string

[Term]
id: GENO:0000343
name: aneusomic chromosomal part
def: "A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation." []
comment: Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome."
is_a: SO:0001059 ! sequence_alteration
relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic
relationship: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "Novel sequence features gained in a genome are considered to be sequence alterations, including aneusomic chromosome segments gained through unbalanced translocation events, entire aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that becoome part of the heritable genome of a cell or organism." xsd:string
property_value: IAO:0000118 "aneuploid chromosomal segment" xsd:string
property_value: IAO:0000118 "aneusomic chromosomal subregion/segment" xsd:string
property_value: IAO:0000118 "partial aneusomic chromosomal element" xsd:string

[Term]
id: GENO:0000344
name: gained aneusomic chromosomal segment
def: "A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event." []
comment: Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location.
is_a: GENO:0000343 ! aneusomic chromosomal part
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000118 "duplicate partial aneuploid chromosomal element" xsd:string
property_value: IAO:0000118 "translocated duplicate chromosomal element" xsd:string
property_value: IAO:0000118 "translocated duplicate chromosomal segment" xsd:string

[Term]
id: GENO:0000345
name: lost aneusomic chromosomal segment
def: "A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome." []
comment: This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event.  The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome.\n\nLoss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.
is_a: GENO:0000343 ! aneusomic chromosomal part
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement" xsd:string
property_value: IAO:0000118 "dropped partial anneuploid chromosomal element" xsd:string
property_value: IAO:0000118 "translocated absent chromosomal segment" xsd:string
property_value: IAO:0000118 "truncated chromosome terminus" xsd:string

[Term]
id: GENO:0000346
name: aneusomic chromosome
def: "A complete chromosome that has been abnormally duplicated, or the absense of a chromosome that has been lost, typically as the result of a non-disjunction event or unbalanced translocation" []
comment: Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism.\n\nSimilarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication.
is_a: SO:0000340 ! chromosome
is_a: SO:0001059 ! sequence_alteration
relationship: GENO:0000207 GENO:0000513 ! has_sequence_attribute aneusomic
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000118 "complete aneusomic chromosome" xsd:string

[Term]
id: GENO:0000351
name: biological process
is_a: BFO:0000015 ! process
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of biological processes from GO-BP." xsd:string

[Term]
id: GENO:0000391
name: disomic zygosity
def: "A zygosity quality inhering in a 'single locus complement' in a genome with a normal ploidy of two (i.e. two copies of autosomal chromosomes). Disomic zygosity terms describe the degree of similarity of the two sequence features that reside at a particular location across homozygous chromosomes (or the state of being the only feature at a given locus in the case of hemizygosity)." []
is_a: GENO:0000133 ! zygosity

[Term]
id: GENO:0000392
name: aneusomic zygosity
def: "A zygosity quality inhering in a 'single locus complement' in a genome with an abnormal ploidy at the location (i.e. an autosomal locus with one or three copies in a diploid genome)." []
is_a: GENO:0000133 ! zygosity

[Term]
id: GENO:0000393
name: trisomic homozygous
is_a: GENO:0000392 ! aneusomic zygosity

[Term]
id: GENO:0000394
name: trisomic heterozygous
is_a: GENO:0000392 ! aneusomic zygosity

[Term]
id: GENO:0000402
name: compound heterozygous
def: "A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>)" []
is_a: GENO:0000135 ! heterozygous
property_value: IAO:0000118 "trans-heterozygous" xsd:string

[Term]
id: GENO:0000415
name: obsolete reagent sequence feature
def: "A sequence feature that references some biological macromolecule applied as a reagent in an experiment or technique (e.g. a morpholino expression plasmid, or oligonucleotide probe)" []
property_value: IAO:0000116 "replaced with SO:engineered_region" xsd:string
property_value: IAO:0000118 "extra-genomic sequence" xsd:string
is_obsolete: true

[Term]
id: GENO:0000458
name: simple heterozygous
comment: a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>)
is_a: GENO:0000135 ! heterozygous

[Term]
id: GENO:0000460
name: transgene part
def: "A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)" []
intersection_of: GENO:0000666 ! gene part
intersection_of: RO:0002525 SO:0000902 ! is subsequence of transgene

[Term]
id: GENO:0000476
name: variant
def: "An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level" []
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000477
name: polymorphic
def: "An attribute inhereing in a sequence feature for which there is more than one version fixed in a population at some significant percentage (typically 1% or greater), where the locus is not considered to be either reference or a variant." []
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000480
name: mutant
def: "An attribute inhering in a feature bearing a sequence alteration that is present at very low levels in a given population (typically less than 1%), or that has been experimentally generated to alter the feature with respect to some reference sequence." []
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000481
name: genomic feature
def: "A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)" []
comment: 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. \n\n2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). \n\n3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.
intersection_of: SO:0000110 ! sequence_feature
intersection_of: GENO:0000903 GENO:0000902 ! has_location genomic feature location
relationship: BFO:0000050 SO:0001026 ! is part of genome
relationship: GENO:0000239 GENO:0000960 ! has_sequence genomic sequence
relationship: RO:0002162 OBI:0100026 ! in taxon organism
property_value: IAO:0000116 "This class was created largely as a modeling convenience to support organizing data for schema definitions.  We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology." xsd:string

[Term]
id: GENO:0000482
name: genetic material
def: "A nucleic acid molecule that contains one or more sequences serving as a template for gene expression in a biological system (ie a cell or virion)." []
comment: This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype.  So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'.  Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material.
is_a: CHEBI:33696 ! nucleic acid
property_value: IAO:0000114 GENO:0000484

[Term]
id: GENO:0000491
name: obsolete mutant allele
def: "An allele that is variant with respect to some wild-type allele, in virtue of its being very rare in a population (typically <1%), or being an experimentally-induced alteration that derives from a wild-type feature in a given strain." []
comment: 'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000119 "Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines" xsd:string
property_value: IAO:0000231 "Not required for any specific use case at this point so removed for simplicity. \nFormely asserted as allele and inferred as varaint allele. \nEq class definition:\nallele\n and (mutation or ('has subsequence' some mutation))" xsd:string
is_obsolete: true

[Term]
id: GENO:0000492
name: mutation
def: "A sequence alteration that is very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type feature in a given strain." []
is_a: SO:0001059 ! sequence_alteration
relationship: GENO:0000683 GENO:0000501 ! varies_with wild-type allele

[Term]
id: GENO:0000494
name: extrachromosomal replicon
def: "A genetic feature that is not part of the chromosomal genome of a cell or virion, but rather a stable and heritable element that is replilcated and passed on to progeny (e.g. a replicative plasmid or transposon)" []
property_value: IAO:0000116 "Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element" xsd:string
property_value: IAO:0000118 "episomal replicon" xsd:string
property_value: IAO:0000231 "Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is novel or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'." xsd:string

[Term]
id: GENO:0000495
name: expression construct
is_a: GENO:0000856 ! engineered genetic construct
property_value: IAO:0000118 "expression construct feature" xsd:string

[Term]
id: GENO:0000497
name: polymorphic allele
def: "An allele that is fixed in a population at some stable level, typically > 1%. Polymorphic alleles reside at loci where more than one version exists at some signifcant frequency in a population." []
comment: Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%).
is_a: GENO:0000512 ! allele
property_value: IAO:0000119 "PMID: 25741868 ACMG Guidelines" xsd:string

[Term]
id: GENO:0000498
name: major polymorphic allele
def: "A polymorphic allele  that is present at the highest frequency relative to other polymorphic variants at the same genomic location." []
is_a: GENO:0000497 ! polymorphic allele
property_value: IAO:0000118 "major allele" xsd:string

[Term]
id: GENO:0000499
name: minor polymorphic allele
def: "A polymorphic allele that is not present at the highest frequency among all fixed variants at the locus (i.e. not the major polymorphic allele at a given location)." []
is_a: GENO:0000497 ! polymorphic allele
property_value: IAO:0000118 "minor allele" xsd:string

[Term]
id: GENO:0000500
name: ancestral polymorphic allele
def: "A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree." []
is_a: GENO:0000497 ! polymorphic allele
property_value: IAO:0000118 "ancestral allele" xsd:string

[Term]
id: GENO:0000501
name: wild-type allele
def: "An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared." []
comment: 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain.\n\nThe notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.
is_a: GENO:0000512 ! allele
relationship: GENO:0000683 GENO:0000481 ! varies_with genomic feature
property_value: IAO:0000118 "wild-type allele" xsd:string

[Term]
id: GENO:0000502
name: wild-type gene
comment: A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation.
is_a: GENO:0000501 ! wild-type allele
is_a: SO:0000704 ! gene
property_value: IAO:0000118 "wild-type gene allele" xsd:string

[Term]
id: GENO:0000504
name: reagent targeted gene
def: "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." []
comment: The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level.  For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position.
is_a: GENO:0000529 ! expression-variant gene
relationship: GENO:0000231 GENO:0000534 ! has_proper_part reagent-targeted gene subregion
relationship: GENO:0000447 GENO:0000533 ! is_gene_target_of gene knockdown reagent

[Term]
id: GENO:0000506
name: transiently-expressed transgene
def: "A transgene that is delivered as part of a DNA expression construct into a cell or organism in order to transiently express a specified product (i.e. it has not integrated into the host genome)." []
is_a: GENO:0000529 ! expression-variant gene
property_value: IAO:0000118 "experimentally-expressed transgene" xsd:string
property_value: IAO:0000118 "extrinsic transgene" xsd:string

[Term]
id: GENO:0000511
name: wild-type
def: "An allele attribute describing a highly common variant (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are compared." []
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000512
name: allele
def: "One of a set of sequence features known to exist at a particular genomic location." []
comment: An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).
intersection_of: GENO:0000481 ! genomic feature
intersection_of: GENO:0000683 GENO:0000481 ! varies_with genomic feature
property_value: IAO:0000116 "A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a].  But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene.\n\nTo be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene.\n	\n[1] https://isogg.org/wiki/Allele (retrieved 2018-03-17)\n[2] http://semanticscience.org/resource/allele (retrieved 2018-03-17)\n[3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17)\n[4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17)\n[5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17)\n[6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17)\n[6a] https://www.ncbi.nlm.nih.gov/mesh/68000483\n[7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17)\n[8]  https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17)\n[9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17)\n[10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17)\n[11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)" xsd:string
property_value: IAO:0000118 "variable feature" xsd:string

[Term]
id: GENO:0000513
name: aneusomic
def: "a sequence attribute of a chromosome or chromosomal region that has been abnormally duplicated or lost, as the result of a non-disjunction event or unbalanced translocation." []
is_a: GENO:0000773 ! variation attribute
property_value: IAO:0000114 GENO:0000484

[Term]
id: GENO:0000515
name: variant gene allele
def: "An allele of a gene that contains some sequence alteration." []
comment: A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard.  But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset.
intersection_of: GENO:0000014 ! gene allele
intersection_of: GENO:0000683 GENO:0000036 ! varies_with reference allele
relationship: GENO:0000382 SO:0001059 ! has_variant_part sequence_alteration
relationship: GENO:0000641 SO:0000704 ! is_variant_allele_of gene

[Term]
id: GENO:0000516
name: single locus complement
def: "A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism." []
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 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes.\n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets  feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene.  The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome.  But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.
is_a: GENO:0000660 ! genomic feature set
property_value: IAO:0000112 "The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>.\n\nThe collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome." xsd:string
property_value: IAO:0000116 "TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label." xsd:string
property_value: IAO:0000118 "allelic complement" xsd:string
property_value: IAO:0000118 "homologous allele complement" xsd:string
property_value: IAO:0000118 "single locus feature complement" xsd:string

[Term]
id: GENO:0000524
name: extrinsic genotype
def: "A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state." []
comment: An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state').  In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease.  It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.
is_a: GENO:0000536 ! genotype
property_value: IAO:0000112 "In an experiment where shha is targeted by MO1 and shhb is overexpressed from a transgenic expression construct, the extrinsic genotype captures the altered expression status of these two genes. A notation for representing such a genotype might describe this scenario as:\n\n   shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb>\n\nThis notation parallels those used for more traditional 'intrinsic' genotypes, where the affected gene is presented with its alteration in angled brackets < >. In the extrinsic genotype shown here, the variation in shha is affected by a specific concentration of an shha-targeting morpholino (instead of a mutation in the shha gene). And the variation in shhb is affected by its overexpression from a pFLAG Shhb expression construct." xsd:string
property_value: IAO:0000116 "We acknowledge that this is not a 'genotype' in the traditional sense, but this terminological choice highlights similarities that play out in parallel modeling of intrinsic and extrinsic genotype partonomies, and parallel syntactic formats for labeling instances of these genotypes. \n\nOur rationale here is that what we care about from perspective of G2P associations is identifying genomic features that impact phenotype - where experimental approaches include permanent introduction of intrinsic modifications to genomic sequence, and transient introduction of extrinsic factors that modify expression of specific genes. As the former is described by the traditional notion of a genotype, it seems a rational leap to consider the latter akin to an 'extrinsic genotype' wherein the alterations are externally  applied rather than inherent to the genome. \n\nFinally, there is some precedent to thinking about such extrinsic modifications in terms of a genotype, in the EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string
property_value: IAO:0000118 "experimental genotype" xsd:string
property_value: IAO:0000118 "expression genotype" xsd:string

[Term]
id: GENO:0000525
name: effective genotype
def: "A genotype that describes the total intrinsic and extrinsic variation across a genome at the time of a phenotypic assessment (where 'intrinsic' refers to variation in genomic sequence, as mediated by sequence alterations, and 'extrinsic' refers to variation in gene expression, as mediated through transient gene-specific interventions such as gene knockdown reagents or overexpression constructs)." []
comment: An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment.
is_a: GENO:0000536 ! genotype
relationship: BFO:0000051 GENO:0000524 ! has part extrinsic genotype
relationship: BFO:0000051 GENO:0000719 ! has part intrinsic genotype
property_value: IAO:0000116 "Closest concept/definition we could find for this concept was for EFO:0000513 ! genotype: \"The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.\"" xsd:string

[Term]
id: GENO:0000527
name: reagent-targeted gene complement
def: "A set comprised of *all* reagent-targeted genes in a single genome in the context of a given experiment (e.g. the zebrafish shha and shhb genes in a zebrafish exposed to morpholinos targeting both of these genes)." []
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. For example, a 'reagent-targeted gene complement' is the set of all genes in a particular genome that are targeted by reagents in the context of a particular experiment.
is_a: GENO:0000715 ! qualified genomic feature set
relationship: RO:0002351 GENO:0000504 ! has member reagent targeted gene

[Term]
id: GENO:0000528
name: transiently-expressed transgene complement
def: "The set of all transgenes trransiently expressed in a biological system in the context of a given experiment." []
is_a: GENO:0000715 ! qualified genomic feature set
relationship: GENO:0000382 GENO:0000506 ! has_variant_part transiently-expressed transgene
property_value: IAO:0000118 "experimental transgene complement" xsd:string

[Term]
id: GENO:0000529
name: expression-variant gene
def: "A gene altered in its expression level relative to some baseline of normal expression in the system under investigation (e.g. a cell line or model organism)." []
comment: Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism).\n\nThe identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system.
is_a: GENO:0000737 ! expression-qualified sequence feature
relationship: GENO:0000443 SO:0000704 ! is_expression_variant_of gene
property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino1 vs  morpholino 2 in separate experiments. These shha genes share identical sequence and position, but represent distinct  instances of a 'expression-variant genes' because of their different external context. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants of the same gene can have potentially different associated phenotypes)." xsd:string
property_value: IAO:0000116 "See SO classes under 'silenced gene' (e.g. 'gene silenced by RNA interference'). These seem to represent the concept of a qualified feature as I define it here, in that they are defined by alterations extrinsic to the sequence and position of the gene itself." xsd:string
property_value: IAO:0000118 "expression allele" xsd:string

[Term]
id: GENO:0000533
name: gene knockdown reagent
is_a: SO:0000804 ! engineered_region
property_value: IAO:0000118 "gene targeting reagent" xsd:string
property_value: IAO:0000118 "sequence targeting reagent" xsd:string

[Term]
id: GENO:0000534
name: reagent-targeted gene subregion
def: "A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent." []
is_a: GENO:0000737 ! expression-qualified sequence feature
property_value: IAO:0000118 "targeted gene segment" xsd:string

[Term]
id: GENO:0000536
name: genotype
def: "A specification of the genetic state of an organism, whether complete (defined over the whole genome) or incomplete (defined over a subset of the genome). Genotypes typically describe this genetic state as a diff between some variant component and a canonical reference." []
comment: 1. Scope of 'Genetic State': \n'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'.  First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs.\n\n2. Genotype Subtypes:\nIn GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes).  We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. \n\nTwo more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome.  In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features.\n\n3. The Genotype Partonomy: \n'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy  of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes.  For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at  zfin.org/ZDB-FISH-150901-9362, include the following elements:\n\n - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome)\n - Genomic Background: AB (the reference against which the GVC is variant)\n - VSLC1:  fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus)\n - VSLC2:  fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus)\n - Allele 1:  fgf8a<ti282a>   (variant version of the fgf8a gene, present in two copies)\n - Allele 2:  fgf3<t24149>    (variant version of the fgf3 gene, present in one copy)\n - Allele 3:   fgf3<+>    (wild-type version of the fgf3 gene, present in one copy)\n - Sequence Alteration1: <ti282a>  (the specific mutation within the fgf8a gene that makes it variant)\n - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant)\n\nA graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md\n\nOne reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000116 "As information artifacts, genotypes specify the state of a genome be defining a diff between some canonical reference and a variant or alternate sequence that replaces the corresponding portion of the reference. We can consider a genotype then as a collection of these reference and variant features, along with some rule for operating on them and resolve a final single sequence. This is valid ontologically because we commit only to sequence features being GDCs - which allows for their concretization in either biological or informational patterns. Accordingly, a particular gene allele, such as shh<tbx292>, can be part of a genome in a biological sense and part of a genotype in an informational sense. This idea underpins the 'genotype partonomy' at the core of the GENO model that decomposes a complete genotype into its more fundamental parts, including alleles and allele complements, as described in the comment above." xsd:string
property_value: IAO:0000119 "Core definition above adapted from the GA4GH VMC data model definition here: https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.4e32jj4jtmsl (retrieved 2018-04-09). \nNote however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO." xsd:string

[Term]
id: GENO:0000575
name: zebrafish phenotype
comment: ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl\nThis ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes.
is_a: UPHENO:0001001 ! Phenotype

[Term]
id: GENO:0000602
name: homoplasmic
def: "an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." []
is_a: GENO:0000918 ! organellar plasmy

[Term]
id: GENO:0000603
name: heteroplasmic
def: "an allelic state where more than one type of allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism." []
is_a: GENO:0000918 ! organellar plasmy

[Term]
id: GENO:0000604
name: hemizygous X-linked
is_a: GENO:0000134 ! hemizygous

[Term]
id: GENO:0000605
name: hemizygous Y-linked
is_a: GENO:0000134 ! hemizygous

[Term]
id: GENO:0000606
name: hemizygous insertion-linked
is_a: GENO:0000134 ! hemizygous

[Term]
id: GENO:0000611
name: genomic background
def: "A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations)." []
intersection_of: GENO:0000899 ! genomic genotype
intersection_of: GENO:0000968 GENO:0000152 ! sequence role reference
relationship: IAO:0000219 GENO:0000010 ! denotes background genome
property_value: IAO:0000116 "Being a 'genomic background' implies that a variant genotype was derived from this background (which is the case for most model organism database genotypes/strains). This is a subtly different notion than being a 'reference genotype' , which can be any genotype that serves as a basis for comparison. But in a sense all background genotypes are by default reference genotypes, in that the derived variant genotype is compared against it." xsd:string
property_value: IAO:0000118 "background genotype" xsd:string

[Term]
id: GENO:0000614
name: chromosomal region
def: "An extended part of a chromosome representing a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band." []
is_a: SO:0000830 ! chromosome part
relationship: BFO:0000050 SO:0000105 ! is part of chromosome arm
property_value: IAO:0000112 "The descriptor 1p22.3 =  chromosome 1, short arm, region 2, band 2, sub-band 3.  This is read as \"one q two-two point three\", not \"one  q twenty-two point three\"." xsd:string
property_value: IAO:0000116 "New term request for SO." xsd:string
property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string

[Term]
id: GENO:0000616
name: chromosome sub-band
is_a: SO:0000830 ! chromosome part
relationship: BFO:0000050 SO:0000341 ! is part of chromosome band
relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity
property_value: IAO:0000112 "The descriptor 1p22.3 =  chromosome 1, short arm, region 2, band 2, sub-band 3.  This is read as \"one q two-two point three\", not \"one  q twenty-two point three\"." xsd:string
property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string

[Term]
id: GENO:0000618
name: chromosomal band intensity
is_a: GENO:0000788 ! sequence feature attribute
property_value: IAO:0000118 "chromosomal band brightness" xsd:string

[Term]
id: GENO:0000619
name: gpos
is_a: GENO:0000618 ! chromosomal band intensity

[Term]
id: GENO:0000620
name: gneg
is_a: GENO:0000618 ! chromosomal band intensity

[Term]
id: GENO:0000621
name: gvar
is_a: GENO:0000618 ! chromosomal band intensity

[Term]
id: GENO:0000622
name: gpos100
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000623
name: gpos75
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000624
name: gpos50
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000625
name: gpos25
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000628
name: short chromosome arm
def: "A chromosome arm that is the shorter of the two arms of a given chromosome." []
is_a: SO:0000105 ! chromosome arm
property_value: IAO:0000118 "p-arm" xsd:string
property_value: IAO:0000118 "stalk" xsd:string

[Term]
id: GENO:0000629
name: long chromosome arm
def: "A chromosome arm that is the longer of the two arms of a given chromosome." []
is_a: SO:0000105 ! chromosome arm
property_value: IAO:0000118 "q-arm" xsd:string

[Term]
id: GENO:0000632
name: gpos66
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000633
name: gpos33
is_a: GENO:0000619 ! gpos

[Term]
id: GENO:0000637
name: regulatory transgene region
def: "A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed." []
is_a: SO:0005836 ! regulatory_region
relationship: RO:0002525 SO:0000902 ! is subsequence of transgene

[Term]
id: GENO:0000638
name: expressed transgene region
def: "A transgene part whose sequence is expressed in a gene product through transcription and/or translation." []
is_a: GENO:0000460 ! transgene part
relationship: RO:0002525 SO:0000902 ! is subsequence of transgene
property_value: IAO:0000118 "coding transgene feature" xsd:string

[Term]
id: GENO:0000640
name: reporter region
is_a: GENO:0000638 ! expressed transgene region

[Term]
id: GENO:0000642
name: selectable marker transgene
def: "A transgene whose product is used as a selectable marker." []
intersection_of: SO:0000902 ! transgene
intersection_of: GENO:0000207 GENO:0000911 ! has_sequence_attribute selectable marker
relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered

[Term]
id: GENO:0000644
name: karyotype
def: "A genotype that describes what is known about variation in a genome at a gross structural level, in terms of the number and appearance of chromosomes in the nucleus of a eukaryotic cell." []
comment: Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations).   \n\nA base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation).
is_a: GENO:0000899 ! genomic genotype
relationship: IAO:0000219 SO:0001026 ! denotes genome
property_value: IAO:0000119 "Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)" xsd:string

[Term]
id: GENO:0000645
name: genomic genotype (sex-qualified)
def: "A genomic genotype where the genomic background specifies a male or female sex chromosome complement." []
comment: We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does.  Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement.  By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances.\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.
is_a: GENO:0000899 ! genomic genotype
relationship: GENO:0000650 GENO:0000000 ! has_sex_agnostic_part genomic genotype (sex-agnostic)
property_value: IAO:0000116 "This modeling approach enables creation separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described.  These sex specific genotypes can be linked to the broader intrinsic genotype that is shared by male 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\nIn 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.  Ontologically, this parthood is based on the fact that the background component of a sex-qualified genotype specifies the sex chromosomes while that of the sex-agnostic genotype does not. Thus, the sequence content of the sex-qualified genotype is a superset of that of the intrinsic genotype, with the latter being a proper part of the former." xsd:string
property_value: IAO:0000118 "intrinsic genotype (sex-specific)" xsd:string
property_value: IAO:0000118 "sex-qualified genotype" xsd:string
property_value: IAO:0000118 "sex-qualified intrinsic genotype" xsd:string

[Term]
id: GENO:0000646
name: male intrinsic genotype
def: "A genomic genotype here the genomic background specifies a male sex chromosome complement." []
is_a: GENO:0000645 ! genomic genotype (sex-qualified)

[Term]
id: GENO:0000647
name: female intrinsic genotype
def: "A genomic genotype here the genomic background specifies a female sex chromosome complement." []
is_a: GENO:0000645 ! genomic genotype (sex-qualified)

[Term]
id: GENO:0000649
name: unspecified genomic background
def: "A background genotype whose sequence or identity is not known or specified." []
is_a: GENO:0000611 ! genomic background
property_value: IAO:0000118 "unspecified background genotype" xsd:string

[Term]
id: GENO:0000659
name: sequence feature set
def: "A set of sequence features." []
comment: 'Sets' are used to represent entities that are typically collections of more than one member. 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'. Sets may also include duplicates (i.e. contain more than one member representing the same feature).\n\nThe notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C\} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome  - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3].\n\n[1] https://www.snpedia.com/index.php/APOE-%CE%B54\n[2] https://www.snpedia.com/index.php/APOE-%CE%B52\n[3] https://www.snpedia.com/index.php/Gs270
is_a: GENO:0000701 ! sequence feature or set
relationship: RO:0002351 SO:0000110 ! has member sequence_feature
property_value: IAO:0000112 "1. The set of all alleles at a particular location in a genome (a 'single locus complement')  - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus\n\n2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele.\n\n3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3,  . . . 22, X, Y}" xsd:string

[Term]
id: GENO:0000660
name: genomic feature set
def: "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.
is_a: GENO:0000659 ! sequence feature set
relationship: RO:0002162 OBI:0100026 ! in taxon organism
relationship: RO:0002351 GENO:0000481 ! has member genomic feature
property_value: IAO:0000116 "In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member." xsd:string
property_value: IAO:0000118 "genomic locus complement" xsd:string

[Term]
id: GENO:0000666
name: gene part
def: "A genomic feature that is part of a gene, and delineated by some functional or structural function or role it serves (e.g.a promoter element, coding region, etc)." []
xref: SO:0000831 (gene member region)
intersection_of: GENO:0000481 ! genomic feature
intersection_of: RO:0002525 GENO:0000014 ! is subsequence of gene allele
property_value: IAO:0000118 "defined gene part" xsd:string

[Term]
id: GENO:0000667
name: reporter transgene
def: "A transgene that codes for a product used as a reporter of gene expression or activity." []
intersection_of: SO:0000902 ! transgene
intersection_of: GENO:0000207 GENO:0000910 ! has_sequence_attribute reporter
relationship: BFO:0000051 GENO:0000640 ! has part reporter region
relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered

[Term]
id: GENO:0000680
name: obsolete null feature
def: "A genomic feature that has an extent of zero." []
property_value: IAO:0000112 "A junction between bases, a deletion variant, a terminus at the end of a chromosome." xsd:string
property_value: IAO:0000116 "Former logical def: \n'genomic feature'\n and (has_extent value 0)" xsd:string
is_obsolete: true

[Term]
id: GENO:0000681
name: novel extrachromosomal replicon
def: "An extrachromosomal replicon that is variant in a genome in virtue of its being a novel addition to the genome - i.e. it is not present in the reference for the genome in which it is found." []
comment: Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.
is_a: GENO:0000684 ! novel replicon
relationship: GENO:0000207 GENO:0000139 ! has_sequence_attribute heritable
relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel
property_value: IAO:0000118 "aberrant extrachromosomal replicon" xsd:string
property_value: IAO:0000118 "exogenous extrachromosomal replicon" xsd:string
property_value: IAO:0000118 "transgenic extrachromosomal replicon" xsd:string

[Term]
id: GENO:0000684
name: novel replicon
def: "A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome." []
comment: Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles.  There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus.  But conceptually, we still consider these to represent genetic variants and classify them as variant alleles.
is_a: SO:0001059 ! sequence_alteration
relationship: GENO:0000207 GENO:0000685 ! has_sequence_attribute novel
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "This class is defined so as to support classification of things like novel extrachromosomal replicons and aneusomic chromosomes as being variant alleles in a genome. These represent entirely new features in the genome - not variants of an existing feature." xsd:string

[Term]
id: GENO:0000685
name: novel
def: "An attribute of a genomic feature that represents a feature not previously found in a given genome, e.g. an extrachromosomal replicon or aneusomic third copy of a chromosome." []
is_a: GENO:0000773 ! variation attribute

[Term]
id: GENO:0000688
name: terminus
def: "A sequence feature representing the end of a sequence that is bounded only on one side (e.g. at the end of an chromosome or oligonucleotide)." []
is_a: SO:0000110 ! sequence_feature

[Term]
id: GENO:0000701
name: sequence feature or set
def: "A sequence feature or a set of such features." []
comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position.  For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.
is_a: BFO:0000031 ! generically dependent continuant
union_of: GENO:0000701 ! sequence feature or set
union_of: SO:0000110 ! sequence_feature
property_value: IAO:0000118 "sequence feature or collection" xsd:string

[Term]
id: GENO:0000702
name: biological sequence
def: "A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides)." []
comment: 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.
xref: VMC:State
is_a: GENO:0000921 ! biological sequence or set
disjoint_from: GENO:0000815 ! sequence feature location
disjoint_from: SO:0000110 ! sequence_feature
property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a  mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string
property_value: IAO:0000118 "biomacromolecular sequence" xsd:string
property_value: IAO:0000118 "state" xsd:string {IAO:0000116="In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele."}

[Term]
id: GENO:0000713
name: qualified sequence feature or collection
def: "A sequence feature (or collection of features) whose identity is dependent on the context or state of its material bearer (in addition to its sequence an position).  This context/state describes factors external to its inherent sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." []
is_a: BFO:0000031 ! generically dependent continuant

[Term]
id: GENO:0000714
name: qualified genomic feature
def: "A qualified sequence feature that carries sequence derived from the genome of a cell or organism." []
is_a: GENO:0000919 ! qualified sequence feature
relationship: GENO:0000726 GENO:0000481 {GENO:0000834="true", comment="Formalizes one identity criteria of the sequence feature component of a qualified sequence feature (which itself is identified by its sequence and its genomic position)."} ! has_sequence_feature genomic feature
relationship: RO:0002162 OBI:0100026 ! in taxon organism
property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string

[Term]
id: GENO:0000715
name: qualified genomic feature set
def: "A set of qualified sequence features that carry genomic sequence." []
comment: A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles \{rs7412-C, rs429358-C\} comprise the haplotype defining the APOEɛ4 gene allele.\n\nA complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome.
is_a: GENO:0000920 ! qualified sequence feature set
relationship: GENO:0000726 GENO:0000660 ! has_sequence_feature genomic feature set
relationship: RO:0002162 OBI:0100026 ! in taxon organism
relationship: RO:0002351 GENO:0000714 ! has member qualified genomic feature
property_value: IAO:0000116 "Because there are cases there may be zero or only one member of such a set, this class is not asserted to necessarily have some 'qualified genomic feature' as a member." xsd:string

[Term]
id: GENO:0000719
name: intrinsic genotype
comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement').  Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference  'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.
is_a: GENO:0000536 ! genotype
property_value: IAO:0000116 "Genotype vs Genome in GENO: An (intrinsic) genotype is an information artifact representing an indirect syntax for specifying a genome sequence.  This syntax has reference and variant components -  a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve a specifie genome sequence.  Specifically, the genome sequence is resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'.  So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when holding that a genotype 'specifies' a genome." xsd:string

[Term]
id: GENO:0000720
name: DNA sequence
intersection_of: GENO:0000702 ! biological sequence
intersection_of: GENO:0000783 GENO:0000780 ! has_sequence_unit DNA residue
intersection_of: GENO:0000783 GENO:0000780 {all_only="true"} ! has_sequence_unit DNA residue

[Term]
id: GENO:0000721
name: RNA sequence
intersection_of: GENO:0000702 ! biological sequence
intersection_of: GENO:0000783 GENO:0000781 ! has_sequence_unit RNA residue
intersection_of: GENO:0000783 GENO:0000781 {all_only="true"} ! has_sequence_unit RNA residue

[Term]
id: GENO:0000722
name: amino acid sequence
intersection_of: GENO:0000702 ! biological sequence
intersection_of: GENO:0000783 GENO:0000782 ! has_sequence_unit amino acid residue
intersection_of: GENO:0000783 GENO:0000782 {all_only="true"} ! has_sequence_unit amino acid residue

[Term]
id: GENO:0000724
name: obsolete biological sequence or collection
is_obsolete: true

[Term]
id: GENO:0000725
name: obsolete biological sequence collection
is_obsolete: true

[Term]
id: GENO:0000736
name: location-qualified sequence feature
def: "A sequence feature whose identity is additionally dependent on  the cellular or anatomical location of the genetic material bearing the feature." []
comment: As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell).
is_a: GENO:0000714 ! qualified genomic feature
property_value: IAO:0000114 GENO:0000484

[Term]
id: GENO:0000737
name: expression-qualified sequence feature
def: "A sequence feature whose identity is additionally dependent on factors specifically influencing its level of expression in the context of a biological system (e.g. being targeted by gene-knockdown reagents, or driven from exogneous expression system like recombinant construct)" []
is_a: GENO:0000714 ! qualified genomic feature

[Term]
id: GENO:0000768
name: obsolete genomic position
def: "A sequence feature position based on a genomic coordinate system, where the position specifies start and end coordinates based on its alignment with some reference genomic sequence." []
property_value: IAO:0000116 "This 'genomic position' concept differs from the faldo:Position concecpt in that the former describes the start AND end points/coordinates of a feature, while the latter describes a single point/coordinate at the beginning OR end of a feature." xsd:string
property_value: IAO:0000118 "genomic coordinates" xsd:string
property_value: IAO:0000231 "remodeling notion of sequence feature position around the idea of a 'genomic locus'" xsd:string
is_obsolete: true

[Term]
id: GENO:0000770
name: phenotypic inheritance process
is_a: GENO:0000351 ! biological process
property_value: IAO:0000114 GENO:0000484

[Term]
id: GENO:0000772
name: obsolete unspecified
def: "A sequence attribute inhering in a feature whose identity is not specified." []
is_obsolete: true

[Term]
id: GENO:0000773
name: variation attribute
def: "An attribute describing a type of variation inhering in a sequence feature or collection." []
is_a: GENO:0000788 ! sequence feature attribute
property_value: IAO:0000118 "allele attribute" xsd:string

[Term]
id: GENO:0000777
name: variant genomic genotype
def: "An intrinsic genotype that specifies variation from a defined reference genome." []
intersection_of: GENO:0000899 ! genomic genotype
intersection_of: IAO:0000219 GENO:0000033 ! denotes variant genome

[Term]
id: GENO:0000778
name: obsolete sequence information entity
def: "An information entity that is intented to represent some biological sequence, sequence feature, qualified sequence feature, or a collection of one or more of these entities." []
property_value: IAO:0000231 "eliminating classes that are not necessary or add uneeded complexity." xsd:string
is_obsolete: true

[Term]
id: GENO:0000779
name: biological sequence unit
property_value: IAO:0000118 "biological sequence residue" xsd:string
property_value: IAO:0000118 "monomeric residue" xsd:string

[Term]
id: GENO:0000780
name: DNA residue
is_a: GENO:0000779 ! biological sequence unit
property_value: IAO:0000118 "deoxyribonucleic acid residue" xsd:string

[Term]
id: GENO:0000781
name: RNA residue
is_a: GENO:0000779 ! biological sequence unit
property_value: IAO:0000118 "ribonucleic acid residue" xsd:string

[Term]
id: GENO:0000782
name: amino acid residue
is_a: GENO:0000779 ! biological sequence unit

[Term]
id: GENO:0000788
name: sequence feature attribute
def: "An attribute, quality, or state of a sequence feature or collection." []
comment: Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase.  Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.
xref: http://purl.obolibrary.org/obo/SO_0000400
is_a: BFO:0000020 ! specifically dependent continuant

[Term]
id: GENO:0000815
name: sequence feature location
def: "The location of a sequence feature as defined by its start and end position on some reference coordinate system." []
comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms).\n\n2. The notion of a sequence feature 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 location 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 locus and the sequence feature that resides there.
is_a: BFO:0000031 ! generically dependent continuant
disjoint_from: SO:0000110 ! sequence_feature

[Term]
id: GENO:0000818
name: modification-qualified sequence feature
def: "A sequence feature whose identity is additionally dependent on a chemical modification made to the genetic material bearing the feature (e.g. binding of transcriptional regulators, or epigenetic modifications including direct DNA methylation, or modification of histones associated with a feature)" []
is_a: GENO:0000714 ! qualified genomic feature
property_value: IAO:0000114 GENO:0000484

[Term]
id: GENO:0000823
name: allelic genotype
def: "A genotype that specifies the 'allelic state' at a particular location in the genome - i.e. the set of alleles present at this locus across all homologous chromosomes." []
comment: An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location.\n\nThis contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background.
intersection_of: GENO:0000719 ! intrinsic genotype
intersection_of: IAO:0000219 GENO:0000516 ! denotes single locus complement
property_value: IAO:0000112 "1. The zebrafish \"fgf8a<ti282a>/fgf8a<+>\" allelic genotype describes the combination of gene alleles present at a specific gene locus (the fgf8a locus -  which here has a heterozygous state).\n\n2. The human allelic genotypes in the VCF records describes below describe the set of SNPs present at specific positions on Chromosome 20 in the human genome. The first record describes a heterozygouse C/T allelic genotype at Chr20:2300608, and the second describes a homozygous G/G allelic genotype at Chr20:2301308.\n\n   ##fileformat=VCFv4.2\n   ##FORMAT=<ID=GT, Description=\"Genotype, 0=REF, 1=ALT\">\n   #CHROM      POS       REF  ALT   FILTER  FORMAT   SAMP001\n        20         2300608    C      T      PASS        GT	         0/1	\n        20         2301308    T      G      PASS        GT	         1/1\n   (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html)\n\n3. Some allelic genotype formats encode the genotype as a single string - e.g.  \"GRCh38 Chr12:258635(A;T)\" describes a heterozygous A/T allelic genotype of SNPs present at a specific position 258635 on human chromosome 12." xsd:string
property_value: IAO:0000118 "single locus genotype" xsd:string

[Term]
id: GENO:0000833
name: genotype-phenotype association
is_a: http://purl.org/oban/association ! association
relationship: GENO:0000580 ENVO:01000254 {GENO:0000834="true"} ! has_qualifier environmental system
relationship: http://purl.org/oban/association_has_object UPHENO:0001001 {GENO:0000834="true"} ! Phenotype
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each." xsd:string

[Term]
id: GENO:0000839
name: knockdown reagent targeted gene complement
is_a: GENO:0000527 ! reagent-targeted gene complement
relationship: GENO:0000382 GENO:0000504 ! has_variant_part reagent targeted gene

[Term]
id: GENO:0000848
name: obsolete coding sequence alteration
def: "A sequence alteration within the coding sequence of a gene." []
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000231 "Not required at this poitn, so marked exploratory and obsoleted.  \nAsserted under sequence_alteration." xsd:string
is_obsolete: true

[Term]
id: GENO:0000850
name: P-element construct
def: "A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome." []
is_a: GENO:0000856 ! engineered genetic construct

[Term]
id: GENO:0000856
name: engineered genetic construct
def: "An engineered region that is used to transfer foreign genetic material into a host cell." []
comment: Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells.  \n\nConstructs are typically packaged as part  of delivery systems such as plasmids or viral vectors.
is_a: SO:0000804 ! engineered_region
property_value: IAO:0000118 "engineered_genetic_vector" xsd:string

[Term]
id: GENO:0000861
name: extra-chromosomal transgene
def: "A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct." []
is_a: SO:0000902 ! transgene
property_value: IAO:0000118 "non-integrated transgene" xsd:string

[Term]
id: GENO:0000870
name: obsolete sequence feature collection
def: "A collection of more than one sequence feature." []
xref: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection
is_obsolete: true

[Term]
id: GENO:0000871
name: haplotype
def: "A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block." []
comment: A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference.  Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. \n\nAs highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\n1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which  collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand.  \n\n2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/).\n\n3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome.   \n\nEach of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.
is_a: GENO:0000660 ! genomic feature set
relationship: RO:0002351 GENO:0000512 ! has member allele
property_value: http://purl.org/dc/terms/source "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype." xsd:string
property_value: IAO:0000116 "Consider if we dont want to define this as a 'complement', as it implies a complet set of memebrs of a defined type.  But many haplotypes will be incomplete, due to lack of knowledge of other variation bound by the haplotype block.\n\nInstead, we can create an 'allele set' class as the haplotype parent?" xsd:string

[Term]
id: GENO:0000872
name: genomic sequence set
def: "A set of genomic sequences (a biological sequence that is of genomic origin)." []
comment: A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. '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. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location.
is_a: GENO:0000922 ! biological sequence set
property_value: IAO:0000118 "copy number complement" xsd:string

[Term]
id: GENO:0000873
name: microsatellite alteration
is_a: GENO:0000874 ! repeat region alteration

[Term]
id: GENO:0000874
name: repeat region alteration
is_a: SO:0001059 ! sequence_alteration

[Term]
id: GENO:0000875
name: allelic state
def: "A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism" []
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: GENO:0000876
name: obsolete genetic dosage
comment: Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nDuplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus.  For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature.  The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities.  The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found.
property_value: IAO:0000118 "allelic dosage" xsd:string
property_value: IAO:0000118 "an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome." xsd:string
property_value: IAO:0000118 "gene dosage" xsd:string
property_value: IAO:0000231 "Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute." xsd:string
is_obsolete: true

[Term]
id: GENO:0000877
name: allele origin
def: "A quality inhering in an allele that describes its genetic origin (how it came to be part of a cell's genome), i.e. whether it occurred de novo through some spontaneous mutation event, or was inherited from a parent." []
is_a: GENO:0000788 ! sequence feature attribute
property_value: IAO:0000118 "genetic origin" xsd:string
property_value: IAO:0000118 "variant origin" xsd:string

[Term]
id: GENO:0000878
name: maternal allele origin
def: "Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg." []
is_a: GENO:0000888 ! germline allele origin
property_value: IAO:0000118 "maternally inherited" xsd:string

[Term]
id: GENO:0000879
name: paternal allele origin
def: "Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm." []
is_a: GENO:0000888 ! germline allele origin
property_value: IAO:0000118 "paternally inherited" xsd:string

[Term]
id: GENO:0000880
name: de novo allele origin
def: "Describes an allele that originated through a mutation event in a germ cell of one of the parents, or in the fertilized egg itself during early embryogenesis. De novo alleles are* heritable* but *not inherited*." []
comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed constitutively  in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. \n		\nDe novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder.
is_a: GENO:0000877 ! allele origin
property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation  and  https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string

[Term]
id: GENO:0000881
name: unknown allele origin
def: "Describes an allele  whose origin is not known." []
is_a: GENO:0000877 ! allele origin

[Term]
id: GENO:0000882
name: somatic allele origin
def: "Describes an allele that result from some spontaneous mutation event in a somatic cell after fertilization, and thus are not present in every cell in the body." []
comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell.  By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells.\n		\nThese acquired mutations are called 'somatic' because they typically affect  somatic (non-germ) cells.  But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations.
is_a: GENO:0000877 ! allele origin
property_value: IAO:0000118 "acquired" xsd:string
property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant  and  https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string

[Term]
id: GENO:0000883
name: obsolete gametic
def: "a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells)." []
property_value: IAO:0000118 "germ-line" xsd:string
property_value: IAO:0000231 "replaced by GENO:0000900 ! 'germline'" xsd:string
is_obsolete: true

[Term]
id: GENO:0000885
name: diplotype
def: "An allelic genotype specifying the set of two alleles present at a particular location in a diploid genome (i.e., a diploid 'single locus complement')\n\nAlt: A sequence feature complement comprised of two haplotypes at a particular location on paired homologous chromosomes in a diploid genome." []
comment: "Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes."\nFrom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/

[Term]
id: GENO:0000886
name: allelic phase
def: "A quality inhering in a collection of discontinuous sequence features in a single genome in virtue of their relative position on the same or separate chromosomes." []
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: GENO:0000887
name: oryzias latipes strain
is_a: GENO:0000112 ! strain or breed
relationship: RO:0002351 NCBITaxon:8090 ! has member Oryzias latipes
relationship: RO:0002351 NCBITaxon:8090 {all_only="true"} ! has member Oryzias latipes

[Term]
id: GENO:0000888
name: germline allele origin
def: "Describes an allele that is inherited from a parent in virtue of the allele being present in the germline of one of the parents." []
comment: We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (present constitutively in a parent and passed down to offspring) and *heritable* (passable down to future offspring).  By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell.  Traits caused by de novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells.
is_a: GENO:0000974 ! inherited allele origin
property_value: IAO:0000118 "hereditary" xsd:string
property_value: IAO:0000118 "parental origin" xsd:string
property_value: IAO:0000118 "parentally inherited" xsd:string
property_value: IAO:0000119 "Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant  and  https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation" xsd:string

[Term]
id: GENO:0000889
name: undetermined inheritance
def: "An inheritance pattern that is not determined or not known." []
is_a: GENO:0000141 ! inheritance pattern
property_value: IAO:0000118 "unknown inheritance" xsd:string

[Term]
id: GENO:0000890
name: obsolete canonical allele
def: "One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model>" []
comment: As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand.\n\nIn the ClinGen allele model, 'canonical alleles  are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)
property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string
property_value: IAO:0000112 "The canonical allele that represents a single nucleotide variation in the BRCA2 gene, which can be described by various contextual alleles such as “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A”." xsd:string
property_value: IAO:0000116 "The notion of a 'canonical allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/).  It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string
property_value: IAO:0000119 "http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/" xsd:string
property_value: IAO:0000231 "No longer needed by  ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs." xsd:string
is_obsolete: true

[Term]
id: GENO:0000891
name: obsolete contextual allele
def: "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 “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.
property_value: http://purl.org/dc/terms/source "ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)" xsd:string
property_value: IAO:0000116 "The notion of a 'contextual allele' is taken from the ClinGen Allele model (http://dataexchange.clinicalgenome.org/allele/).  It is implemented in GENO to provide an ontological representation of this concept that will support data integration efforts, but may be replaced by should an IRI become available from the ClinGen model." xsd:string
property_value: IAO:0000119 "http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/" xsd:string
property_value: IAO:0000231 "No longer needed by  ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.\n\nFormer axiom: denotes some 'obsolete_canonical allele'" xsd:string
is_obsolete: true

[Term]
id: GENO:0000892
name: heteroplasmic mitochondrial inheritance
def: "A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not." []
is_a: GENO:0000949 ! mitochondrial inheritance

[Term]
id: GENO:0000893
name: homoplasmic mitochondrial inheritance
def: "A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited." []
is_a: GENO:0000949 ! mitochondrial inheritance

[Term]
id: GENO:0000897
name: genomic entity
def: "An generically dependent continuant that carries biological sequence that is part of or derived from a genome." []
is_a: BFO:0000031 ! generically dependent continuant
relationship: RO:0002162 OBI:0100026 ! in taxon organism
property_value: GENO:0000905 "true" xsd:boolean
property_value: IAO:0000116 "An abstract/organizational class to support data modeling, that includes genomic features, genomic feature complements, qualified genomic features and their complements, as well as genotypes that denote such entities." xsd:string

[Term]
id: GENO:0000898
name: haplotype block
def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations." []
comment: A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'.  The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations.  A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.
is_a: GENO:0000481 ! genomic feature
property_value: IAO:0000116 "Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as \n\"A genomic location over which there is little evidence for historical recombination, such that sequence alterations it contains are typically co-inherited across generations.\" Look at how teh concept is used in research, and if people think of each version of sequence in a haplotype block to be an instance. I think we would just call these versions 'alleles', and then  could define haplotype block as a location.\n\nCurrent definition is based on http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block (def = A region of the genome which is co-inherited as the result of the lack of historic recombination within it). If we stick with a region-level treatment, consdier if as a defined region of genomic sequence where variation is known to occur, a haplotype block should be classified as a subtype of allele." xsd:string
property_value: IAO:0000119 "Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and  DOI: 10.1126/science.1069424." xsd:string

[Term]
id: GENO:0000899
name: genomic genotype
def: "A genotype that describes the total variation in heritable genomic sequence of a cell or organism, typically in terms of alterations from some reference or background genotype." []
comment: 1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement').  Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference  'genomic background' sequence.\n\n2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.
intersection_of: GENO:0000719 ! intrinsic genotype
intersection_of: IAO:0000219 SO:0001026 ! denotes genome
relationship: GENO:0000385 GENO:0000611 ! has_reference_part genomic background
property_value: IAO:0000116 "'Genomic Genotype' vs 'Genome' in GENO: \nA genomic genotype is an information artifact with a representational syntax that can specify what is known about the complete sequence of a genome. This syntax describes 'reference' and 'variant' components - namely a 'background genotype' and 'genomic variation complement' - that must be operated on to resolve the genome sequence.  Specifically, the genome sequence is determined by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'background genotype'.  So, while the total sequence content described in a genotype may exceed that of a single a genome (in that it includes a reference genome and variatoin complement), the intended resolution of these sequences is to arrive at a single genome sequence. It is this end-point that we consider when asserting that a genotype 'specifies' a genome." xsd:string
property_value: IAO:0000118 "complete genotype" xsd:string

[Term]
id: GENO:0000901
name: obsolete allele cellular context
def: "A quality inhering in a particular allele in virtue of its presence only in a particular type of cell in an organism (e.g. somatic vs germ cells)" []
comment: Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.
property_value: IAO:0000231 "decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin" xsd:string
is_obsolete: true

[Term]
id: GENO:0000902
name: genomic feature location
def: "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	\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.
xref: VMC:Location
is_a: GENO:0000815 ! sequence feature location
property_value: IAO:0000116 "In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest.  We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future.\n\nWe don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences." xsd:string
property_value: IAO:0000116 "In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class.   The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed.\n\nFor example, we would define an  'HLA gene block' as a subclass of 'genomic feature', and assert that  HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus'  and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus)." xsd:string
property_value: IAO:0000118 "genomic location" xsd:string
property_value: IAO:0000118 "genomic locus" xsd:string

[Term]
id: GENO:0000904
name: organismal entity
def: "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc)." []
is_a: BFO:0000040 ! material entity
property_value: GENO:0000905 "true" xsd:boolean
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000116 "useful organizational term to collect entities that have genomes/genotypes." xsd:string

[Term]
id: GENO:0000907
name: gene product
def: "The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)" []
is_a: SO:0000110 ! sequence_feature

[Term]
id: GENO:0000910
name: reporter
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: GENO:0000911
name: selectable marker
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: GENO:0000912
name: selectable marker region
is_a: GENO:0000638 ! expressed transgene region

[Term]
id: GENO:0000914
name: reference genome
def: "A genome whose sequence is identical to that of a genome sequence considered to be the reference." []
is_a: SO:0001026 ! genome
relationship: GENO:0000239 SO:0001505 ! has_sequence reference genome sequence

[Term]
id: GENO:0000915
name: obsolete haplotype
def: "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it." []
comment: 1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene':  a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.  In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction.  A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand.  \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome.  \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated).  This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand.  \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene.  In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.
property_value: IAO:0000116 "Former comment: \"Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case - e.g. 'SNP allele' haplotypes are identified and analysed in studies to uncover the genetic basis of common disease by efforts like the International HapMap Project.\"" xsd:string
property_value: IAO:0000119 "Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype." xsd:string
property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.\n\nFormer SC axioms:\n- is_allele_of some 'haplotype block'\n- 'has part' some sequence_alteration" xsd:string
is_obsolete: true

[Term]
id: GENO:0000916
name: obsolete haplotype block
def: "A sequence feature representing a region of the genome over which there is little evidence for historical recombination, such that sequences it contain are typically co-inherited/transmitted across generations." []
comment: A haplotype block is a class of genomic sequence defined by a  lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains.  In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while  a 'haplotype' is one of many possible instances of a 'haplotype block'.\n\nThe boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.\n\n-----------------------\n\n* One difference however is that gene instnaces are necessarily 'functional' - so non-functional  alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces.
property_value: IAO:0000119 "Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block." xsd:string
property_value: IAO:0000231 "Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets." xsd:string
is_obsolete: true

[Term]
id: GENO:0000918
name: organellar plasmy
def: "An allelic state that describes the number of different alleles of a gene from an organellar genome (i.e. mitochondrial, plastid) that may exist in a cell." []
comment: Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of  different origins may contain more than one allele of a given organellar gene.
is_a: GENO:0000875 ! allelic state

[Term]
id: GENO:0000919
name: qualified sequence feature
def: "A sequence feature whose identity is additionally dependent on the context or state of the material sequence molecule in which the feature is concretized. This context/state describes factors external to the feature's intrinsic  sequence and position that can influences its expression, such as being targeted by gene-knockdown reagents, or an epigenetic modification." []
comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a  mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
comment: Modeling sequence entities at this 'qualified' level is useful for distinguishing cases where features with identical sequence and position as separate instances - based on their material bearers being found in different contexts. For example, consider a situation where the zebrafish shha gene (a sequence feature) is targeted in two experimental groups of fish by two different morpholinos, and phenotypes are assessed for each.  We want to be able to represent two 'variants' of the shha gene in this scenario as separate 'qualified sequence feature' instances so we can capture data about the phenotypes resulting from each - just as we would separately represent to different sequence variants (alleles) of the shha gene at the sequence feature level so that we can track their associated phenotypes.
is_a: GENO:0000713 ! qualified sequence feature or collection
property_value: IAO:0000112 "Consider wild-type zebrafish shha gene in the context of being targeted by morpholino MO-1 vs morpholino MO-2 in separate experiments. These shha genes share identical sequence and position, but represent distinct instances of a 'qualified sequence feature' because of their different external contexts. This is important because these qualified features could have distinct phenotypes associated with them (just as two different sequence variants (alleles) of the same gene can have potentially different associated phenotypes)." xsd:string

[Term]
id: GENO:0000920
name: qualified sequence feature set
def: "A set of qualified seqeunce features." []
comment: 'Sets' are used to represent entities that are typically collections of more than one member. 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 'matehmatical sets'.
is_a: GENO:0000713 ! qualified sequence feature or collection
relationship: BFO:0000051 GENO:0000919 ! has part qualified sequence feature
relationship: GENO:0000726 GENO:0000659 ! has_sequence_feature sequence feature set

[Term]
id: GENO:0000921
name: biological sequence or set
def: "A biolocical sequence, or set of such sequences." []
is_a: BFO:0000031 ! generically dependent continuant
property_value: IAO:0000118 "biological sequence or collection" xsd:string

[Term]
id: GENO:0000922
name: biological sequence set
def: "A set of biological sequences." []
comment: 'Sets' are used to represent entities that are typically collections of more than one member. 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'. \n\nA set may also include multiple copies of the same sequence. For example, in a 'copy number complement', members are all copies of this same biological sequence.
is_a: GENO:0000921 ! biological sequence or set

[Term]
id: GENO:0000923
name: obsolete functional copy number complement
def: "A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome." []
comment: As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides.  But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location.  A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele.  This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage).
comment: The notion of 'functional copy number' (aka 'genetic dosage') describes how many 'functional' copies of a sequence are present in a genome - i.e. sequences that retain their normal activity and/or produce gene products that retain their normal activity.  In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This latter condition sets it apart from the notion of a 'copy number complement', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its genomic sequence complement count (i.e. its copy number), but not increase its dosage.
property_value: IAO:0000116 "Formerly considered modeling this as an informational entity, defined as \"An information entity that describes the total number of functional copies of a gene or region of sequence in a particular genome.\"" xsd:string
property_value: IAO:0000118 "functional feature complement" xsd:string
property_value: IAO:0000118 "genetic dosage" xsd:string
property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963." xsd:string
is_obsolete: true

[Term]
id: GENO:0000924
name: obsolete intrinsic sequence feature attribute
def: "A sequence feature attribute that reflects feature-level characteristics that depend only on the sequence, location, or genomic context of a feature  or  collection, but are independent of how it may be concretized in physical form." []
is_obsolete: true

[Term]
id: GENO:0000925
name: obsolete extrinsic sequence feature attribute
def: "A sequence feature attribute that reflects characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, etc.)" []
is_obsolete: true

[Term]
id: GENO:0000926
name: allelic cellular distribution
def: "A quality inhering in an allele reflecting whether it is found in all cells of an organism's body, or just some clonal subset (e.g. in mosaicism)." []
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: GENO:0000927
name: constitutional
def: "A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin." []
is_a: GENO:0000926 ! allelic cellular distribution

[Term]
id: GENO:0000928
name: clonal
def: "A cellular distribuution in which an allele is found only in some clonal subset of cells in an organism, typically in virtue of its somatic origin." []
is_a: GENO:0000926 ! allelic cellular distribution

[Term]
id: GENO:0000929
name: multifactorial inheritance
def: "An inheritance pattern that depends on a mixture of major and minor genetic determinants (i.e. alleles of more than one contributing genes), possibly together with environmental factors." []
comment: Diseases inherited in this manner are termed 'complex diseases'.
xref: http://purl.obolibrary.org/obo/HP_0001426
is_a: GENO:0000141 ! inheritance pattern
property_value: IAO:0000118 "complex inherritance" xsd:string
property_value: IAO:0000118 "multi-factorial inheritance" xsd:string
property_value: IAO:0000118 "multi-genic inheritance" xsd:string
property_value: IAO:0000118 "multi-locus inheritance" xsd:string
property_value: IAO:0000118 "multigenic inheritance" xsd:string

[Term]
id: GENO:0000930
name: digenic inheritance
def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes." []
xref: http://purl.obolibrary.org/obo/HP_0010984
is_a: GENO:0000929 ! multifactorial inheritance

[Term]
id: GENO:0000931
name: oligogenic inheritance
def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes." []
comment: It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform.
xref: http://purl.obolibrary.org/obo/HP_0010983
is_a: GENO:0000929 ! multifactorial inheritance

[Term]
id: GENO:0000932
name: polygenic inheritance
def: "A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes." []
comment: Typically used for traits/conditions governed by more than three gene loci.
xref: http://purl.obolibrary.org/obo/HP_0010982
is_a: GENO:0000929 ! multifactorial inheritance

[Term]
id: GENO:0000933
name: monogenic inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors." []
is_a: GENO:0000141 ! inheritance pattern
property_value: IAO:0000118 "single-gene inheritance" xsd:string

[Term]
id: GENO:0000934
name: autosomal inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome." []
is_a: GENO:0000933 ! monogenic inheritance

[Term]
id: GENO:0000935
name: allosomal inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome." []
xref: http://purl.obolibrary.org/obo/HP_0010985
is_a: GENO:0000933 ! monogenic inheritance
property_value: IAO:0000118 "gonosomal inheritance" xsd:string

[Term]
id: GENO:0000936
name: X-linked inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome." []
xref: http://purl.obolibrary.org/obo/HP_0001417
is_a: GENO:0000935 ! allosomal inheritance

[Term]
id: GENO:0000937
name: complete X-linked dominant inheritance
def: "An X-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." []
is_a: GENO:0000146 ! X-linked dominant inheritance

[Term]
id: GENO:0000938
name: incomplete X-linked dominant inheritance
def: "An X-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." []
is_a: GENO:0000146 ! X-linked dominant inheritance
property_value: IAO:0000118 "semi-dominant X-linked inheritance" xsd:string

[Term]
id: GENO:0000939
name: co-dominant X-linked inheritance
def: "An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." []
is_a: GENO:0000146 ! X-linked dominant inheritance

[Term]
id: GENO:0000941
name: Y-linked inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome." []
xref: http://purl.obolibrary.org/obo/HP_0001450
is_a: GENO:0000935 ! allosomal inheritance
property_value: IAO:0000118 "holandric inheritance" xsd:string

[Term]
id: GENO:0000942
name: Z-linked inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome." []
is_a: GENO:0000935 ! allosomal inheritance

[Term]
id: GENO:0000943
name: Z-linked dominant inheritance
def: "A Z-linked inheritance pattern wherein the trait manifests in heterozygotes." []
is_a: GENO:0000942 ! Z-linked inheritance

[Term]
id: GENO:0000944
name: complete Z-linked dominant inheritance
def: "A Z-linked dominant inheritance pattern wherein the trait associated with one allele completely masks the trait associated with a different allele found at that locus." []
is_a: GENO:0000943 ! Z-linked dominant inheritance

[Term]
id: GENO:0000945
name: incomplete Z-linked dominant inheritance
def: "A Z-linked dominant inheritance pattern wherein the trait expressed in a heterozygous individual is intermediate between the trait expressed in individuals homozygous for either allele in the heterozygous locus." []
is_a: GENO:0000943 ! Z-linked dominant inheritance
property_value: IAO:0000118 "semi-dominant Z-linked inheritance" xsd:string

[Term]
id: GENO:0000946
name: co-dominant Z-linked inheritance
def: "An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus." []
is_a: GENO:0000943 ! Z-linked dominant inheritance

[Term]
id: GENO:0000947
name: Z-linked reccessive inheritance
def: "A Z-linked inheritance pattern wherein a trait caused by alleles of a gene on the Z-chromosome manifests in homozygous but not heterozygote individuals." []
is_a: GENO:0000942 ! Z-linked inheritance

[Term]
id: GENO:0000948
name: W-linked inheritance
def: "An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome." []
is_a: GENO:0000935 ! allosomal inheritance

[Term]
id: GENO:0000949
name: mitochondrial inheritance
def: "An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome." []
comment: Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy).
xref: http://purl.obolibrary.org/obo/HP_0001427
is_a: GENO:0000141 ! inheritance pattern

[Term]
id: GENO:0000952
name: sex-limited autosomal dominant inheritance
def: "An autosomal dominant inheritance pattern wherein the trait manifests in heterozygotes in a sex-specific manner (i.e. only in males or only in females)." []
xref: http://purl.obolibrary.org/obo/HP_0001470
is_a: GENO:0000147 ! autosomal dominant inheritance

[Term]
id: GENO:0000953
name: sex-limited autosomal recessive inheritance
def: "An autosomal recessive inheritance pattern wherein the trait manifests only in homozygotes, and in a sex-specific manner (i.e. only in males or only in females)." []
xref: http://purl.obolibrary.org/obo/HP_0031362
is_a: GENO:0000148 ! autosomal recessive inheritance

[Term]
id: GENO:0000954
name: allele set
def: "A set of discrete alleles within a particular genome." []
comment: 'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member.  An "Allele Set'  represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping  When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'.  When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'.
is_a: GENO:0000660 ! genomic feature set

[Term]
id: GENO:0000955
name: obsolete variant copy number complement
def: "A copy number complement' that has an abnormal number of members (e.g. more or less than two for an autosomal sequence in a diploid genome, as a result of deletion or duplication event(s)." []
comment: In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members.  A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s).\n\nNote that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class.
property_value: IAO:0000118 "copy number variation" xsd:string
property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level." xsd:string
is_obsolete: true

[Term]
id: GENO:0000956
name: obsolete copy number complement
def: "A set of all features in a particular genome whose sequence aligns with a particular location on a reference genome.  Such features are typically on the scale of complete genes or larger." []
comment: 1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles.  \n\n2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence.  So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location.\n\n3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members.  A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members.
property_value: IAO:0000231 "Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961." xsd:string
is_obsolete: true

[Term]
id: GENO:0000960
name: genomic sequence
def: "A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)." []
comment: A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.
is_a: GENO:0000702 ! biological sequence

[Term]
id: GENO:0000961
name: copy number complement
def: "A set representing the complement of all copies of a particular biological sequence (typically at the scale of complete genes or larger) present in a particular genome." []
comment: The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result.\n\nA 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set 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, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. \n\nThe fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene.  The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome.  But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.
comment: The notion of a 'complement' is useful as a special case of a set, where the members necessarily comprise an exhaustive collection of *all* objects that make up some well-defined set. Here, a 'copy number complement' represents 'represents the set of *all* copies of a specified sequence in a particular genome. Note that sequences can be duplicated in a set (i.e. contain more than one member representing the same sequence). In the 'copy number complement' example, each set member is a copy of this same biological sequence.
is_a: GENO:0000872 ! genomic sequence set
property_value: IAO:0000116 "The identity of a 'copy number complement' instance is determined by the sequence defining its members, and their count (the number of times this sequence appears in a particular genome). In reality the sequence of each copy may not be identical, given the tendency of large regions to accumulate subtle variations. What matters is that they share a common origin/alignment with a defining location in a reference genome.\n\nWe represent the notion of copy number at the \"sequence level\" (as opposed to the \"sequence feature level\")  because we are concerned only with the number of copies of a sequence in a genome, and not the location of the features bearing this sequence. Consider a copy number complement comprised of three copies of the sequence defined by the location Chr8 100000-200000 on a GRCh38.2 reference genome.  In one person's genome, this sequence may appear at its normal location on Chromosome 8, as well as in duplications on chromosomes 5, and 12. In another genome the sequence might appear three times as well, but on chromosomes 8, 9, and 15.  When representing causal associations linking copy number to disease, it is important that these are considered to be *the same* copy number complement - because what a curator associates with a disease is the presence of three copies of some sequence in a genome, independent of their location. The \"sequence level\" representation here supports this use case.  By contrast, a \"feature level\" representation, where identity of a copy number complement would be based on the identity of member *features*), does not - because we have two sets comprised of entirely different features (based on location being tied to their identity)." xsd:string

[Term]
id: GENO:0000962
name: variant copy number complement
def: "A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s)." []
comment: 'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome.
is_a: GENO:0000961 ! copy number complement
property_value: IAO:0000116 "Note that this 'variant copy number complement' class in GENO is related to but ontologically distinct from the SO 'copy number variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set departs from the genome's normal ploidy of sequences at that location. The SO class, which is defined as a \"sequence feature level\" concept (and therefore represents a single continuous extent of sequence), refers to a sequence alteration such as a deletion or duplication that changes the copy number of the affected sequence, and would result in the presence of  a 'variant copy number complement'.  The presence of an SO 'copy number variation' suggests, but does not guarantee, the existence of a GENO 'variant copy number complement' (e.g. if a second balancing event has occurred).\n\nFor example, the deletion variant reported in the ClinVar record here (https://www.ncbi.nlm.nih.gov/clinvar/variation/21009/) is a copy number variation in the SO sense - a deletion that likely results in a GENO 'variant copy number complement'. Databases like ClinVar and dbVar type such alterations as 'copy number variants'.  But ClinVar also describes 'variant copy number complements' that may result from the presence of one or more SO 'copy number variations' in a given genome, e.g. here ( https://www.ncbi.nlm.nih.gov/clinvar/variation/221691/).  In this case, the submitter is asserting that a state in which only one copy of the defined sequence (Chr2: 73601366 - 73673202) exists in a genome is pathogenic for 'Premature ovarian failure'.  This requires more knowledge of the complete genomic state than an assertion that a specific SO 'copy number variation' (here, a deletion variant) is pathogenic for the condition - as here we know that not only is one copy deleted, but also that only one copy remains." xsd:string

[Term]
id: GENO:0000963
name: functional copy complement
def: "A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome." []
comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set 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, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence.\n\n'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage.\n\nAs we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides.  But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location.  A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele.
is_a: GENO:0000872 ! genomic sequence set
property_value: IAO:0000118 "functional genetic dosage" xsd:string

[Term]
id: GENO:0000964
name: mosaic
comment: A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type.
is_a: GENO:0000928 ! clonal

[Term]
id: GENO:0000965
name: sequence interval
def: "A pair of integers representing start and end position of a location on a sequence coordinate system." []
is_a: IAO:0000030 ! information content entity

[Term]
id: GENO:0000969
name: chromosomal inheritance
def: "An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors." []
is_a: GENO:0000141 ! inheritance pattern
property_value: IAO:0000119 "The Alliance of Genomic Resources" xsd:string

[Term]
id: GENO:0000970
name: chromosomal deletion inheritance
def: "An inheritance pattern wherein the trait is determined by inheritance of missing sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." []
is_a: GENO:0000969 ! chromosomal inheritance
property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string

[Term]
id: GENO:0000971
name: chromosomal duplication inheritance
def: "An inheritance pattern wherein the trait is determined by inheritance of duplicated sections of one or more chromosomes, encompassing either 0 or multiple genes, possibly together with environmental factors." []
is_a: GENO:0000969 ! chromosomal inheritance
property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string

[Term]
id: GENO:0000972
name: chromosomal rearrangement inheritance
def: "An inheritance pattern wherein the trait is determined by inheritance of translocation or inversion of sections of one or more chromosomes, possibly together with environmental factors." []
is_a: GENO:0000969 ! chromosomal inheritance
property_value: IAO:0000119 "Alliance of Genomic Resources" xsd:string

[Term]
id: GENO:0000974
name: inherited allele origin
def: "Describes an allele that is inherited from a parent." []
is_a: GENO:0000877 ! allele origin
property_value: IAO:0000114 "exploratory" xsd:string
property_value: IAO:0000116 "Need to consider if/how this is different than 'germline allele origin'.\n\nOne scenario that potentially distinguishes them is the case where a de novo mutation occurs in the germ cells of a parent, and is passed to offspring.  This does not qualify as 'germline allele origin', as currently defined.  But it would qualify as 'inherited'" xsd:string

[Term]
id: GENO:0000975
name: uniparental allele origin
def: "Describes an allele that is part of an allelic complement where both alleles are inherited from the same parent." []
comment: From Wikidedia: Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father. This phenomenon is most commonly observed in eukaryotic organelles such as mitochondria and chloroplasts. \nhttps://en.wikipedia.org/wiki/Uniparental_inheritance
is_a: GENO:0000974 ! inherited allele origin
property_value: IAO:0000114 "exploratory" xsd:string

[Term]
id: GENO:0000976
name: biparental allele origin
def: "Describes an allele that is part of an allelic complement where one allele is maternally inherited  and other paternally inherited." []
comment: Biparental inheritance of alleles is typical of normal mendelian inheritance, where offspring inherit a maternal and a paternal copies of a given gene.
is_a: GENO:0000974 ! inherited allele origin
property_value: IAO:0000114 "exploratory" xsd:string

[Term]
id: GENO:0000978
name: nullizygous
def: "A disomic zygosity quality inhering in a 'single locus complement' that is comprised of two non-functional copies of a gene. Loss of function may result from the gene being entirely missing via a deletion, or mutated in a way that eliminates its function." []
synonym: "homozygous null" NARROW []
is_a: GENO:0000391 ! disomic zygosity

[Term]
id: GO:0032502
name: developmental process
def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. [database_cross_reference: GOC:isa_complete]" []
is_a: GENO:0000351 ! biological process

[Term]
id: HP:0000118
name: human phenotypic abnormality
comment: pulling in HP 'phenotypic abnormality' root here
is_a: UPHENO:0001001 ! Phenotype

[Term]
id: HsapDv:0000000
name: human life cycle stage
is_a: GENO:0000351 ! biological process
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of human  developmental stages from the Human Developmental Stages Ontology." xsd:string
property_value: IAO:0000119 "A spatiotemporal region encompassing some part of the life cycle of an organism." xsd:string

[Term]
id: IAO:0000030
name: information content entity
def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" []
is_a: BFO:0000031 ! generically dependent continuant
property_value: IAO:0000111 "information content entity" xsd:string
property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string
property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string
property_value: IAO:0000119 "OBI_0000142" xsd:string

[Term]
id: IAO:0000102
name: data about an ontology part
is_a: IAO:0000030 ! information content entity
property_value: IAO:0000118 "ontology metadata" xsd:string

[Term]
id: MP:0000001
name: mammalian phenotype
comment: where to place this depends on if we take the organismal view or the quality centric view.
is_a: UPHENO:0001001 ! Phenotype

[Term]
id: NCBITaxon:10090
name: Mus musculus
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:10239
name: Viruses
comment: Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:7955
name: Danio rerio
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:8090
name: Oryzias latipes
is_a: OBI:0100026 ! organism

[Term]
id: NCBITaxon:9606
name: Homo sapiens
is_a: OBI:0100026 ! organism

[Term]
id: OBI:0000011
name: planned process
def: "A processual entity that realizes a plan which is the concretization of a plan specification." []
is_a: BFO:0000015 ! process
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for experimental techniques and processes, defined in GENO or imported from ontologies such as OBI and ERO." xsd:string

[Term]
id: OBI:0000086
name: reagent role
is_a: BFO:0000023 ! role

[Term]
id: OBI:0000181
name: population
def: "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area" []
is_a: GENO:0000113 ! taxonomic group

[Term]
id: OBI:0100026
name: organism
is_a: BFO:0000040 ! material entity
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy." xsd:string

[Term]
id: PATO:0000016
name: obsolete color brightness
property_value: IAO:0000116 "'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html" xsd:string
property_value: IAO:0000116 "Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute." xsd:string
property_value: IAO:0000118 "color value" xsd:string
is_obsolete: true

[Term]
id: PATO:0000383
name: female
is_a: PATO:0001894 ! phenotypic sex

[Term]
id: PATO:0000384
name: male
is_a: PATO:0001894 ! phenotypic sex

[Term]
id: PATO:0001894
name: phenotypic sex
is_a: BFO:0000019 ! quality

[Term]
id: PCO:0000000
name: collection of organisms
def: "A material entity that consists of two or more organisms, viruses, or viroids." []
comment: A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role).
is_a: BFO:0000040 ! material entity
relationship: RO:0002351 OBI:0100026 ! has member organism

[Term]
id: PCO:0000020
name: family
def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." []
is_a: PCO:0000000 ! collection of organisms

[Term]
id: Position
name: Position
def: "Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate." []
is_a: GENO:0000902 ! genomic feature location
property_value: IAO:0000116 "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)." xsd:string
property_value: IAO:0000412 "FALDO" xsd:string

[Term]
id: Region
name: Region
def: "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." []
is_a: SO:0000110 ! sequence_feature
relationship: begin Position {cardinality="1"} ! Position
relationship: end Position {cardinality="1"} ! Position
property_value: IAO:0000116 "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." xsd:string

[Term]
id: ReverseStrandPosition
name: Negative strand
is_a: StrandedPosition ! Stranded position

[Term]
id: SO:0000034
name: morpholino_oligo
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." []
is_a: GENO:0000533 ! gene knockdown reagent

[Term]
id: SO:0000105
name: chromosome arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." []
is_a: SO:0000830 ! chromosome part
relationship: BFO:0000050 SO:0000830 ! is part of chromosome part
property_value: IAO:0000112 "The descriptor 1p22.3 =  chromosome 1, short arm, region 2, band 2, sub-band 3.  This is read as \"one q two-two point three\", not \"one  q twenty-two point three\"." xsd:string
property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term." xsd:string
property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band" xsd:string

[Term]
id: SO:0000110
name: sequence_feature
def: "Any extent of continuous biological sequence." []
comment: A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position.  Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.
is_a: GENO:0000701 ! sequence feature or set
relationship: GENO:0000239 GENO:0000702 {GENO:0000834="true", comment="Formalizes the first identity criteria for a sequence feature of its sequence."} ! has_sequence biological sequence
relationship: GENO:0000903 GENO:0000815 {GENO:0000834="true", comment="Formalizes the second identify criteiria for a sequence feature of its genomic position. We use the FALDO model to represent positional information, which links features to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence. (But features can also be linked to Positions directly through the location property)."} ! has_location sequence feature location
property_value: IAO:0000116 "GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria.\n1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence.\n2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology).\n3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a  mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern)." xsd:string

[Term]
id: SO:0000143
name: obsolete assembly_component
def: "A region of known length which may be used to manufacture a longer region." []
is_obsolete: true

[Term]
id: SO:0000149
name: obsolete contig
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." []
is_obsolete: true

[Term]
id: SO:0000159
name: deletion
def: "The point at which one or more contiguous nucleotides were excised." []
xref: http://en.wikipedia.org/wiki/Nucleotide_deletion
is_a: SO:0001059 ! sequence_alteration
property_value: http://purl.obolibrary.org/obo/IAO_alt_id "SO:1000033" xsd:string
property_value: IAO:0000118 "deleted_sequence" xsd:string
property_value: IAO:0000118 "nucleotide deletion" xsd:string
property_value: IAO:0000118 "nucleotide_deletion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0000165
name: enhancer
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000167
name: promoter
def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000199
name: translocation
def: "A region of nucleotide sequence that has translocated to a new position." []
is_a: SO:0001059 ! sequence_alteration
property_value: IAO:0000118 "transchr" xsd:string
property_value: IAO:0000118 "translocated sequence" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0000207
name: simple_sequence_length_variation
is_a: SO:0000248 ! sequence_length_variation
property_value: IAO:0000118 "simple sequence length polymorphism" xsd:string
property_value: IAO:0000118 "simple sequence length variation" xsd:string
property_value: IAO:0000118 "SSLP" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0000248
name: sequence_length_variation
is_a: SO:1000002 ! substitution
property_value: IAO:0000118 "sequence length variation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0000281
name: engineered_foreign_gene
is_a: SO:0000704 ! gene
relationship: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered
property_value: IAO:0000116 "See here for a list of engineered regions in ZFIN: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerselect.apg&marker_type=REGION&query_results=t&compare=contains&WINSIZE=25.\n\nIncludes things like loxP sites, inducible promoters, ires elements, etc." xsd:string

[Term]
id: SO:0000289
name: microsatellite
def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." []
comment: A defined feature that includes any type of VNTR or SSLP locus.
is_a: GENO:0000481 ! genomic feature
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29" xsd:string

[Term]
id: SO:0000337
name: RNAi_reagent
is_a: GENO:0000533 ! gene knockdown reagent

[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." []
comment: A complete chromosome sequence.
is_a: GENO:0000481 ! genomic feature

[Term]
id: SO:0000341
name: chromosome band
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." []
comment: "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.
is_a: SO:0000830 ! chromosome part
relationship: BFO:0000050 GENO:0000614 ! is part of chromosomal region
relationship: GENO:0000207 GENO:0000618 ! has_sequence_attribute chromosomal band intensity
property_value: IAO:0000112 "The descriptor 1p22.3 =  chromosome 1, short arm, region 2, band 2, sub-band 3.  This is read as \"one q two-two point three\", not \"one  q twenty-two point three\"." xsd:string
property_value: IAO:0000119 "http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation and http://people.rit.edu/rhrsbi/GeneticsPages/Handouts/ChromosomeNomenclature.pdf, both of which define the nomenclature for the banding hierarchy we use here:\nchromosome > arm > region > band > sub-band\n\nNote that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html):\nchromosome > arm > band > sub-band > sub-sub-band\n" xsd:string

[Term]
id: SO:0000577
name: centromere
is_a: SO:0000830 ! chromosome part

[Term]
id: SO:0000637
name: obsolete engineered_plasmid
property_value: IAO:0000116 "Obsoleted as we didnt want to commit to constructs being plasmids - but rather wanted a classification of more general types of engineered regions used to replicate and deliver sequence to target cells/genomes. Replaced by GENO:0000856 ! engineered genetic construct." xsd:string
is_obsolete: true

[Term]
id: SO:0000667
name: insertion
def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." []
is_a: SO:0001059 ! sequence_alteration
property_value: http://purl.obolibrary.org/obo/IAO_alt_id "SO:1000034" xsd:string
property_value: IAO:0000118 "insertion" xsd:string
property_value: IAO:0000118 "nucleotide insertion" xsd:string
property_value: IAO:0000118 "nucleotide_insertion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." []
is_a: SO:0001483 ! SNV
property_value: IAO:0000118 "single nucleotide polymorphism" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0000699
name: junction
comment: A junction is a boundary between regions. A boundary has an extent of zero.
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0000704
name: gene
def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." []
comment: A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion.
is_a: GENO:0000481 ! genomic feature
property_value: IAO:0000116 "Regarding the distinction between a 'gene' and a 'gene allele': \nEvery 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)." xsd:string

[Term]
id: SO:0000771
name: QTL
def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." []
is_a: GENO:0000481 ! genomic feature
property_value: IAO:0000118 "quantitative trait locus" xsd:string

[Term]
id: SO:0000783
name: engineered
def: "An attribute to describe a region that was modified in vitro." []
is_a: GENO:0000788 ! sequence feature attribute

[Term]
id: SO:0000804
name: engineered_region
intersection_of: SO:0000110 ! sequence_feature
intersection_of: GENO:0000207 SO:0000783 ! has_sequence_attribute engineered
property_value: IAO:0000118 "construct" xsd:string

[Term]
id: SO:0000830
name: chromosome part
def: "An extended region of sequence corresponding to a defined feature that is a proper part of a chromosome, e.g. a chromosomal 'arm', 'region', or 'band'." []
intersection_of: GENO:0000481 ! genomic feature
intersection_of: GENO:0000248 SO:0000340 ! is_proper_part_of chromosome
property_value: IAO:0000118 "chromosomal feature" xsd:string
property_value: IAO:0000118 "gross chromosomal part" xsd:string

[Term]
id: SO:0000902
name: transgene
def: "A gene that has been transferred naturally or by any of a number of genetic engineering techniques into a cell or organism where it is foreign (i.e. does not belong to the host genome)." []
comment: On the relationship between 'transgenic insertions', 'transgenes', and 'alleles'\nTransgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species  as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome.  In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome.  But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene  traps) to complete.\n\nIn addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference.  An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele.  \n\nFor the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion.  The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains.  The model of the Flybase example HERE illustrates this approach.
comment: Transgenes can exist as integrated into the host genome, or extra-chromosomally on replicons or transiently carried/expressed vectors.  What matters is that they are active in the context of a foreign biological system (typically a cell or organism).\n\nNote that transgenes as defined here are not necessarily from a different taxon than that of the host genome.  For example, a Mus musculus gene over-expressed from a chromosomally-integrated expression construct in a Mus musculus genome qualifies as a transgene because it is exogenous to the host genome.
is_a: SO:0000704 ! gene

[Term]
id: SO:0001013
name: MNP
def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." []
is_a: SO:1000002 ! substitution
property_value: IAO:0000118 "multiple nucleotide polymorphism" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0001019
name: copy_number_variation
def: "A variation that increases or decreases the copy number of a given region." []
xref: http://en.wikipedia.org/wiki/Copy_number_variation
is_a: SO:0001059 ! sequence_alteration
property_value: IAO:0000118 "CNP" xsd:string
property_value: IAO:0000118 "CNV" xsd:string
property_value: IAO:0000118 "copy number polymorphism" xsd:string
property_value: IAO:0000118 "copy number variation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0001026
name: genome
def: "A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)" []
comment: A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.
is_a: GENO:0000660 ! genomic feature set
relationship: RO:0002162 OBI:0100026 ! in taxon organism
property_value: IAO:0000116 "Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence.  This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence." xsd:string
property_value: IAO:0000118 "'genome sequence'" xsd:string

[Term]
id: SO:0001059
name: sequence_alteration
def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." []
comment: 1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. \n\nAlleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part.\n\n2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence).  In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. \n\nFor a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference.\n\n3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism.
intersection_of: GENO:0000512 ! allele
intersection_of: GENO:0000784 GENO:0000481 ! completely_varies_with genomic feature
property_value: http://purl.obolibrary.org/obo/IAO_alt_id "SO:1000004" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_alt_id "SO:1000007" xsd:string
property_value: IAO:0000112 "A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': \n\n1. Consider NM_000059.3(BRCA2):c.631G>A variation in the BRCA2 gene.  This mutation of a single nucleotide creates a gene allele whose extent is that of the entire BRCA2 gene.  This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the single altered base is a 'sequence alteration'.  See https://www.ncbi.nlm.nih.gov/snp/80358871.\n\n2. Consider the NM_000059.3(BRCA2):c.132_133ins8 variation in the BRCA2 gene.  This 8 bp insertion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the extent of sequence spanning just the 8 bp insertion is a 'sequence alteration'.   See https://www.ncbi.nlm.nih.gov/snp/483353112.\n\n3. Consider the NM_000059.3(BRCA2):c.22_23delAG variation in the BRCA2 gene.  This 2 bp deletion creates a gene allele whose extent is that of the entire BRCA2 gene. This version of the full BRCA2 gene is a 'variant allele', while the junction where the deletion occured is a 'sequence alteration' with an extent of zero.  See https://www.ncbi.nlm.nih.gov/snp/483353112." xsd:string
property_value: IAO:0000118 "sequence variation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0001218
name: transgenic_insertion
def: "An insertion that derives from another organism, via the use of recombinant DNA technology." []
is_a: SO:0000667 ! insertion
relationship: BFO:0000051 GENO:0000093 ! has part integrated transgene
property_value: IAO:0000118 "transgenic insertion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0001410
name: obsolete experimental_feature
def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." []
property_value: IAO:0000231 "not currently needed to support modeling use cases. can re-introduce if becomes necessary." xsd:string
is_obsolete: true

[Term]
id: SO:0001477
name: gene_trap_construct
def: "A construct which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." []
is_a: GENO:0000856 ! engineered genetic construct

[Term]
id: SO:0001478
name: promoter_trap_construct
def: "A construct which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." []
is_a: GENO:0000856 ! engineered genetic construct

[Term]
id: SO:0001479
name: enhancer_trap_construct
def: "A construct which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." []
is_a: GENO:0000856 ! engineered genetic construct

[Term]
id: SO:0001483
name: SNV
def: "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist." []
is_a: SO:1000002 ! substitution
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Thu Oct 08 11:37:49 PDT 2009" xsd:string
property_value: IAO:0000118 "single nucleotide variant" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:0001500
name: heritable_phenotypic_marker
def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." []
is_a: GENO:0000481 ! genomic feature

[Term]
id: SO:0001505
name: reference genome sequence
def: "A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced." []
is_a: GENO:0000017 ! reference sequence
relationship: GENO:0000968 GENO:0000152 ! sequence role reference
property_value: IAO:0000112 "'GRCh37.p10' (a human reference genome build)" xsd:string

[Term]
id: SO:0001742
name: copy_number_gain
def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." []
is_a: SO:0001019 ! copy_number_variation
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:54:09 PST 2011" xsd:string
property_value: IAO:0000118 "copy number gain" xsd:string
property_value: IAO:0000118 "gain" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0001743
name: copy_number_loss
def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." []
is_a: SO:0001019 ! copy_number_variation
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 01:55:02 PST 2011" xsd:string
property_value: IAO:0000118 "copy number loss" xsd:string
property_value: IAO:0000118 "loss" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0001744
name: UPD
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." []
xref: http:http\\\://en.wikipedia.org/wiki/Uniparental_disomy
is_a: SO:0001059 ! sequence_alteration
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:01:05 PST 2011" xsd:string
property_value: IAO:0000118 "uniparental disomy" xsd:string
property_value: IAO:0000118 "UPD" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0001745
name: maternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." []
is_a: SO:0001744 ! UPD
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:01 PST 2011" xsd:string
property_value: IAO:0000118 "maternal uniparental disomy" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0001746
name: paternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." []
is_a: SO:0001744 ! UPD
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Mon Feb 28 02:03:30 PST 2011" xsd:string
property_value: IAO:0000118 "paternal uniparental disomy" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:0001784
name: complex_structural_alteration
def: "A structural sequence alteration where there are multiple equally plausible explanations for the change." []
is_a: SO:0001785 ! structural_alteration
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Wed Mar 23 03:21:19 PDT 2011" xsd:string
property_value: IAO:0000118 "complex" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0001785
name: structural_alteration
is_a: SO:0001059 ! sequence_alteration
property_value: http://purl.obolibrary.org/obo/IAO_created_by "kareneilbeck" xsd:string
property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Fri Mar 25 02:27:41 PDT 2011" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: SO:0005836
name: regulatory_region
is_a: GENO:0000666 ! gene part
property_value: IAO:0000116 "Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term." xsd:string
property_value: IAO:0000118 "regulatory element" xsd:string
property_value: IAO:0000118 "regulatory gene region" xsd:string

[Term]
id: SO:1000002
name: substitution
def: "Any change in genomic DNA caused by a single event." []
is_a: SO:0001059 ! sequence_alteration
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change." []
is_a: SO:1000002 ! substitution
property_value: IAO:0000118 "complex substitution" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:1000008
name: point_mutation
def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." []
xref: http://en.wikipedia.org/wiki/Point_mutation
is_a: SO:0001483 ! SNV
property_value: IAO:0000118 "point mutation" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." []
is_a: SO:0001483 ! SNV
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." []
is_a: SO:1000009 ! transition
property_value: IAO:0000118 "pyrimidine transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." []
is_a: SO:1000010 ! pyrimidine_transition
property_value: IAO:0000118 "C to T transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." []
is_a: SO:1000011 ! C_to_T_transition
property_value: IAO:0000118 "C to T transition at pCpG site" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000013
name: T_to_C_transition
is_a: SO:1000010 ! pyrimidine_transition
property_value: IAO:0000118 "T to C transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." []
is_a: SO:1000009 ! transition
property_value: IAO:0000118 "purine transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." []
is_a: SO:1000014 ! purine_transition
property_value: IAO:0000118 "A to G transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." []
is_a: SO:1000014 ! purine_transition
property_value: IAO:0000118 "G to A transition" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." []
xref: http://en.wikipedia.org/wiki/Transversion
is_a: SO:0001483 ! SNV
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." []
is_a: SO:1000017 ! transversion
property_value: IAO:0000118 "pyrimidine to purine transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
property_value: IAO:0000118 "C to A transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000020
name: C_to_G_transversion
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
property_value: IAO:0000118 "C to G transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
property_value: IAO:0000118 "T to A transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
property_value: IAO:0000118 "T to G transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." []
is_a: SO:1000017 ! transversion
property_value: IAO:0000118 "purine to pyrimidine transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
property_value: IAO:0000118 "A to C transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
property_value: IAO:0000118 "A to T transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
property_value: IAO:0000118 "G to C transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
property_value: IAO:0000118 "G to T transversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000032
name: indel
def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." []
comment: Indels can have a different number of bases than the corresponding reference sequence.
xref: http://en.wikipedia.org/wiki/Indel
is_a: SO:0001059 ! sequence_alteration
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000035
name: duplication
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." []
is_a: SO:0000667 ! insertion
property_value: IAO:0000118 "nucleotide duplication" xsd:string
property_value: IAO:0000118 "nucleotide_duplication" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." []
is_a: SO:0001059 ! sequence_alteration
property_value: IAO:0000118 "inversion" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string
property_value: IAO:subset "SOFA" xsd:string

[Term]
id: SO:1000039
name: direct_tandem_duplication
def: "A tandem duplication where the individual regions are in the same orientation." []
is_a: SO:1000173 ! tandem_duplication
property_value: IAO:0000118 "direct tandem duplication" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000040
name: inverted_tandem_duplication
def: "A tandem duplication where the individual regions are not in the same orientation." []
is_a: SO:1000173 ! tandem_duplication
property_value: IAO:0000118 "inverted tandem duplication" xsd:string
property_value: IAO:0000118 "mirror duplication" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl

[Term]
id: SO:1000173
name: tandem_duplication
def: "A duplication consisting of 2 identical adjacent regions." []
is_a: SO:1000035 ! duplication
property_value: IAO:0000118 "erverted" xsd:string
property_value: IAO:0000118 "tandem duplication" xsd:string
property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl
property_value: IAO:subset "DBVAR" xsd:string

[Term]
id: StrandedPosition
name: Stranded position
comment: 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'.
is_a: Position ! Position

[Term]
id: UBERON:0000105
name: life cycle stage
is_a: GENO:0000351 ! biological process
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or  taxon specific vocabularies such as ZFIN stages terms)" xsd:string

[Term]
id: UBERON:0001062
name: anatomical entity
xref: http://purl.obolibrary.org/obo/CARO_0000000
is_a: BFO:0000040 ! material entity
relationship: RO:0001000 OBI:0100026 ! derives from organism
property_value: IAO:0000116 "Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies." xsd:string

[Term]
id: UPHENO:0001001
name: Phenotype
comment: 1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition)\n\n2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment
is_a: BFO:0000020 ! specifically dependent continuant
property_value: IAO:0000116 "Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework." xsd:string

[Term]
id: WBPhenotype:0000886
name: worm phenotype
def: "Animals exhibit variations compared to a given control." []
is_a: UPHENO:0001001 ! Phenotype
property_value: IAO:0000116 "'Variant' is the given label of the root class in the Worm Phenotype ontology.  Renamng it here to be consisent with our hierarchy of phenotype classes." xsd:string
property_value: IAO:0000118 "c. elegans phenotype" xsd:string
property_value: IAO:0000118 "Variant" xsd:string

[Term]
id: ZP:0000199
name: abnormal(ly) malformed endocardium cell
is_a: GENO:0000575 ! zebrafish phenotype

[Term]
id: ZP:0000386
name: abnormal(ly) absent dorso-rostral cluster
is_a: GENO:0000575 ! zebrafish phenotype

[Term]
id: ZP:0000755
name: abnormal(ly) disrupted  diencephalon development
is_a: GENO:0000575 ! zebrafish phenotype

[Term]
id: ZP:0005531
name: abnormal(ly) disrupted neutrophil aggregation
is_a: GENO:0000575 ! zebrafish phenotype

[Term]
id: ZP:0005692
name: abnormal(ly) absent adaxial cell
is_a: GENO:0000575 ! zebrafish phenotype

[Term]
id: http://purl.org/oban/association
name: association
is_a: IAO:0000030 ! information content entity

[Term]
id: http://www.ncbi.nlm.nih.gov/gene/20423
name: mus musculus shh gene
comment: Equivalent to: http://www.informatics.jax.org/marker/MGI:98297
is_a: GENO:0000057 ! mus musculus gene
property_value: IAO:0000114 GENO:0000514

[Term]
id: http://www.ncbi.nlm.nih.gov/gene/30269
name: danio rerio shha gene
xref: http://zfin.org/ZDB-GENE-980526-166
is_a: GENO:0000047 ! danio rerio gene
property_value: IAO:0000114 GENO:0000514

[Term]
id: http://www.ncbi.nlm.nih.gov/gene/399483
name: danio rerio cdkn1ca gene
xref: http://zfin.org/ZDB-GENE-040123-1
is_a: GENO:0000047 ! danio rerio gene
property_value: IAO:0000114 GENO:0000514

[Term]
id: http://www.ncbi.nlm.nih.gov/gene/6469
name: homo sapiens SHH gene
comment: Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690\n\nCodes for: http://www.uniprot.org/uniprot/Q15465
is_a: GENO:0000054 ! homo sapiens gene
property_value: IAO:0000114 GENO:0000514

[Typedef]
id: BFO:0000050
name: is part of
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part

[Typedef]
id: BFO:0000051
name: has part
is_transitive: true
is_a: RO:0002131 ! overlaps

[Typedef]
id: GENO:0000207
name: has_sequence_attribute
def: "A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'." []
xref: http://purl.obolibrary.org/obo/so_has_quality
property_value: IAO:0000116 "Used in lieu of RO/BFO has_quality as this relation is definend to apply to independent contiinuant bearers, wheras sequence entities are generically dependent continuants." xsd:string

[Typedef]
id: GENO:0000211
name: bears_concretization_of
def: "A relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes" []
comment: Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.
property_value: IAO:0000118 "materializes" xsd:string
holds_over_chain: RO:0000053 RO:0000059

[Typedef]
id: GENO:0000220
name: is_genotype_of
inverse_of: GENO:0000222 ! has_genotype

[Typedef]
id: GENO:0000222
name: has_genotype
def: "A relationship that holds between a biological entity and some level of genetic variation present in its genome." []
comment: The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or  biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.
property_value: IAO:0000116 "This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype." xsd:string

[Typedef]
id: GENO:0000231
name: has_proper_part
def: "An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)" []
xref: http://semanticscience.org/resource/SIO_000053
property_value: IAO:0000116 "No proper part relation anymore in RO/BFO?" xsd:string
is_transitive: true
is_a: BFO:0000051 ! has part
inverse_of: GENO:0000248 ! is_proper_part_of

[Typedef]
id: GENO:0000239
name: has_sequence
def: "A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears." []
comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.
xref: VMC:state
property_value: IAO:0000118 "has_sequence_component" xsd:string
property_value: IAO:0000118 "has_state" xsd:string
range: GENO:0000702 ! biological sequence
inverse_of: GENO:0000251 ! is_sequence_of

[Typedef]
id: GENO:0000242
name: obsolete_specifies
def: "A relationship between an information content entity representing a specification, and the entity it specifies." []
property_value: IAO:0000112 "A geno:intrinnsic genotype 'specifies' a SO:genome.\nA geno:karyotype 'specifies' a geno:karyotype feature collection." xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000243
name: obsolete_approximates_sequence
property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000244
name: obsolete_resolves_to_sequence
property_value: IAO:0000116 "Created subproperties 'approximates_sequence' and 'resolves to sequence'. Genotypes and other sequence variant artifacts are not always expected to completely specify a sequence, but rather provide some approximation based on available knowledge. The 'resolves_to_sequence' property can be used when the sequence variant artifact is able to completely resolve a sequence, and the 'approximates_sequence' property can be used when it does not. " xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000248
name: is_proper_part_of
def: "An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole." []
xref: http://semanticscience.org/resource/SIO_000093
is_a: BFO:0000050 ! is part of

[Typedef]
id: GENO:0000251
name: is_sequence_of
domain: GENO:0000702 ! biological sequence

[Typedef]
id: GENO:0000252
name: is_subject_of
inverse_of: IAO:0000136 ! is about

[Typedef]
id: GENO:0000253
name: obsolete_is_specified_by
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000359
name: obsolete_is_phenotype_of_genotype
def: "shortcut relation used to link a phenotype directly to a genotype of an organism" []
comment: Might expand to something like:\n\nphenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))
property_value: IAO:0000118 "is_phenotype_of_organism_with_genotype" xsd:string
property_value: IAO:0000118 "is_phenotype_with_genotype" xsd:string
property_value: IAO:0000118 "phenotype_has_genotype" xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000368
name: obsolete_participates_in_inheritance_process
def: "A relation to link variant loci, phenotypes, or disease to the type of inheritance process they are involved in, based on how the genetic interactions between alleles at the causative locus determine the pattern of inheritance of a specific phenotype/disease from one generation to the next." []
property_value: IAO:0000116 "Exploratory/temporary property, as we formalize our phenotypic inheritance model." xsd:string
range: GENO:0000141 ! inheritance pattern
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000382
name: has_variant_part
def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is variant in terms of its sequence, position, or expression." []
is_transitive: true
is_a: GENO:0000654 ! has_sequence_part
inverse_of: GENO:0000383 ! is_variant_part_of

[Typedef]
id: GENO:0000383
name: is_variant_part_of
is_transitive: true
is_a: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: GENO:0000385
name: has_reference_part
def: "A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant." []
property_value: IAO:0000118 "has_reference_sequence_part" xsd:string
is_transitive: true
is_a: GENO:0000654 ! has_sequence_part
inverse_of: GENO:0000387 ! is_reference_part_of

[Typedef]
id: GENO:0000387
name: is_reference_part_of
is_a: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: GENO:0000408
name: is_allele_of
def: "A relation linking an instance of a variable feature (aka an allele) to a genomic location/locus it occupies. This is typically a gene locus, but a feature may be an allele of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size." []
comment: To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size).\n\nWhile conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene).  Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of  the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides.  Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene).\n\nIt is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. \n\nThis departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry.  For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the  S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\\GAL4 gene.\n\nAt the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'.
property_value: IAO:0000112 "<fgf8a^ti282a>  is_allele_of  the 'danio rerio fgf8a' gene locus." xsd:string
property_value: IAO:0000116 "Domain = allele \nRange = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation)." xsd:string
property_value: IAO:0000116 "Note that  the allele <fgf8a^ti282a>  is not necessarily an instance of the danio rerio fgf8a gene class, given that we adopt the SO definition of genes as 'producing a functional product'.  If the <fgf8a^ti282a> allele is nonfunctional or null, it is an allele_of the danio rerio fgf8a gene class, but not an instance (rdf:type) of this class. It would, however, bean instance of  a  'danio rerio fgf8a gene allele' class - because being a 'gene allele' as defined in GENO requires only occupying the genomic position where for a gene, but not necessarily producing a functional product." xsd:string
property_value: IAO:0000118 "is_sequence_variant_of" xsd:string
domain: GENO:0000481 ! genomic feature
is_a: GENO:0000418 ! has_affected_feature
inverse_of: GENO:0000413 ! has_allele

[Typedef]
id: GENO:0000410
name: obsolete_is_genetic_variant_of
def: "A relation used to link a variant locus instance to the gene class it is a variant of (in terms of its sequence or expression level)." []
comment: Domain = genomic feature instance\nRange = punned gene class IRI
property_value: IAO:0000118 "is_variant_instance_of" xsd:string
property_value: IAO:0000231 "formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)" xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000411
name: obsolete_has_genetic_variant
def: "A relation linking a gene class to a sequence-varaint or expression-variant of the gene." []
comment: Domain = punned gene class\nRange = genomic feature
property_value: IAO:0000118 "has_variant_instance" xsd:string
property_value: IAO:0000231 "formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)" xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000413
name: has_allele
def: "A relation linking a gene class to one of its sequence-variant alleles." []
property_value: IAO:0000116 "Domain = punned gene class\nRange = allele" xsd:string
property_value: IAO:0000118 "has_sequence_variant" xsd:string
is_a: GENO:0000445 ! is_feature_affected_by

[Typedef]
id: GENO:0000414
name: targets_gene
def: "A relation between a gene targeting reagent (e.g. a morpholino or RNAi) and the class of gene it targets." []
comment: This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets.
is_a: GENO:0000418 ! has_affected_feature
inverse_of: GENO:0000447 ! is_gene_target_of

[Typedef]
id: GENO:0000418
name: has_affected_feature
def: "A relation that holds between an instance of a geneetic variation and a genomic feature (typically a gene class) that is affected in its sequence or expression." []
comment: This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset.
holds_over_chain: GENO:0000382 GENO:0000418
holds_over_chain: GENO:0000383 GENO:0000418
inverse_of: GENO:0000445 ! is_feature_affected_by

[Typedef]
id: GENO:0000443
name: is_expression_variant_of
def: "A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents." []
comment: This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class.
property_value: IAO:0000116 "Domain = expression variant feature.\nRange = punned gene class" xsd:string
is_a: GENO:0000418 ! has_affected_feature
inverse_of: GENO:0000449 ! has_expression_variant

[Typedef]
id: GENO:0000445
name: is_feature_affected_by
def: "A relation between a genomic feature class (typically a gene class) and an instance of a sequence feature or qualified sequence feature that represents or affects some change in the sequence or expression of the genomic feature." []
comment: This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)
property_value: IAO:0000118 "class_to_feature_relation" xsd:string

[Typedef]
id: GENO:0000447
name: is_gene_target_of
def: "A relation between a gene class and a gene targeting reagent that targets it." []
comment: Domain = punned gene class\nRange = gene knockdown reagent
property_value: IAO:0000118 "is_target_of" xsd:string
is_a: GENO:0000445 ! is_feature_affected_by

[Typedef]
id: GENO:0000449
name: has_expression_variant
def: "A relation linking a gene class to one of an expression-variant of that gene.." []
property_value: IAO:0000116 "Domain = punned gene class\nRange = expression variant feature" xsd:string
property_value: IAO:0000118 "has_expression_variant_instance" xsd:string
is_a: GENO:0000445 ! is_feature_affected_by

[Typedef]
id: GENO:0000486
name: obsolete_is_variant_with
def: "A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression." []
comment: This proeprty is most commonly used to relate two different alleles of a given gene.  It is not a relation between an allele and the gene it is a variant of.
property_value: IAO:0000231 "Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property." xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000488
name: obsolete_is_expression_variant_with
def: "A relation between two instances of a given gene that vary in their level of expression as a result of external factors influencing expression (e.g. gnee-knockdown reagents, epigenetic modification, alteration of endogenous gene-regulation pathways)." []
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000580
name: has_qualifier
def: "A relation used to describe  a context or conditions that define and/or identify an entity." []
property_value: IAO:0000116 "Used in Monarch Data to link associations to qualifying contexts (e.g. environments or developmental stages) where the association applies. For example, a qualifying environment represents a context where genotype-phenotype associations apply - where the environment is an identity criteria for the association.\n\nUsed in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features." xsd:string
property_value: IAO:0000118 "has_qualifying_context" xsd:string

[Typedef]
id: GENO:0000608
name: has_zygosity
def: "a relation to link a single locus complement to its zygosity." []
domain: GENO:0000516 ! single locus complement
range: GENO:0000133 ! zygosity
is_a: GENO:0000207 ! has_sequence_attribute

[Typedef]
id: GENO:0000610
name: is_reference_allele_of
def: "A relationship between a reference locus/allele and the gene class it is an allele of." []
domain: GENO:0000036 ! reference allele
is_a: GENO:0000408 ! is_allele_of

[Typedef]
id: GENO:0000626
name: has_staining_intensity
comment: Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized.
property_value: IAO:0000116 "Consider obsoleting - it is likely sufficeint to use the parent has_sequence_attribute property - a separate proeprty to link to the staining intensity attribute is not really needed." xsd:string
property_value: IAO:0000118 "has_color_value" xsd:string
is_a: GENO:0000207 ! has_sequence_attribute

[Typedef]
id: GENO:0000634
name: is_targeted_by
def: "relation between an molecular agent and its molecular target" []
property_value: IAO:0000112 "Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant." xsd:string

[Typedef]
id: GENO:0000639
name: sequence_derives_from
def: "Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence." []
property_value: IAO:0000112 "1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. \n\n2. Used to specify the genetic background/strain of origin of an allele  (i.e. that an allele was originally isolated from a specific background strain, and propagated into new genetic backgrounds.\n\n3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)" xsd:string
holds_over_chain: BFO:0000051 GENO:0000639

[Typedef]
id: GENO:0000641
name: is_variant_allele_of
def: "A relationship between a variant allele and the gene class it is an allele of." []
domain: GENO:0000002 ! variant allele
is_a: GENO:0000408 ! is_allele_of

[Typedef]
id: GENO:0000650
name: has_sex_agnostic_part
property_value: IAO:0000116 "Relationship between a sex-qualified genotype and intrinsic genotype, created specifically to support propagation of phenotypes asserted on the former to the later for Monarch Initiative use cases." xsd:string
is_a: GENO:0000654 ! has_sequence_part
inverse_of: GENO:0000661 ! is_sex_agnostic_part_of

[Typedef]
id: GENO:0000651
name: is_mutant_allele_of
comment: A relation between a mutant allele (ie rare variant present in less than  1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of.
domain: GENO:0000491 ! obsolete mutant allele
is_a: GENO:0000641 ! is_variant_allele_of

[Typedef]
id: GENO:0000652
name: is_polymorphic_allele_of
def: "A relationship between a polymorphic allele and the gene class it is an allele of." []
domain: GENO:0000497 ! polymorphic allele
is_a: GENO:0000641 ! is_variant_allele_of

[Typedef]
id: GENO:0000653
name: is_wild_type_allele_of
def: "A relationship between a wild-type allele and the gene class it is an allele of." []
domain: GENO:0000501 ! wild-type allele
is_a: GENO:0000408 ! is_allele_of

[Typedef]
id: GENO:0000654
name: has_sequence_part
def: "An organizational class to hold relations of parthood between sequences/features." []
is_a: BFO:0000051 ! has part
inverse_of: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: GENO:0000655
name: is_sequence_part_of
is_a: BFO:0000050 ! is part of

[Typedef]
id: GENO:0000661
name: is_sex_agnostic_part_of
def: "Relationship between an intrinsic genotype and a sex-qualified genotype, created specifically to support propagation of phenotypes asserted on the latter to the former for Monarch Initiative use cases." []
is_a: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: GENO:0000683
name: varies_with
def: "A relation that holds between two sequence features at a particular genomic location that vary in their sequence.  These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part)." []
comment: This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene).  It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)
is_symmetric: true

[Typedef]
id: GENO:0000708
name: faldo properties
comment: organizational property to hold imports from faldo.

[Typedef]
id: GENO:0000726
name: has_sequence_feature
def: "A relation linking a qualified sequence feature to its component sequence feature." []
comment: In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.
property_value: IAO:0000118 "has_sequence_feature_component" xsd:string
range: SO:0000110 ! sequence_feature

[Typedef]
id: GENO:0000740
name: has_inferred_phenotype
holds_over_chain: GENO:0000382 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."}
holds_over_chain: GENO:0000383 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."}
holds_over_chain: GENO:0000413 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from a (sequence-)variant locus instance to a gene class (to support cases where the phenotype association is made at the level of the variant gene locus)."}
holds_over_chain: GENO:0000449 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations from an expression-variant gene instance to a gene class (to support cases where the phenotype association is made at the level of the expression-variant gene)."}
holds_over_chain: GENO:0000661 GENO:0000743 {comment="Property chain to propagate inferred phenotype associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"}
is_a: RO:0002200 ! has phenotype

[Typedef]
id: GENO:0000741
name: obsolete_has_regulatory_part
comment: Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000742
name: obsolete_is_alteration_within
def: "A relation linking a sequence_alteration to the gene it alters." []
property_value: IAO:0000114 GENO:0000484
property_value: IAO:0000118 "is_within_allele_of" xsd:string
holds_over_chain: GENO:0000383 GENO:0000408
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000743
name: has_asserted_phenotype
is_a: RO:0002200 ! has phenotype

[Typedef]
id: GENO:0000761
name: is_regulatory_part_of
property_value: IAO:0000116 "Proposal for a property linking regulatory elements to larger features of which they are a part." xsd:string
is_a: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: GENO:0000767
name: obsolete_has_position_component
def: "A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances." []
property_value: IAO:0000116 "For representing positional data, we advocate use of the FALDO model, which links to positional information through an instance of a Region class that represents the mapping of the feature onto some reference sequence.  The positional_component property in GENO is meant primarily to formalize the identity criteria or sequence features and qualified sequence features, to illustrate the distinction between them." xsd:string
is_a: ObsoleteProperty
is_obsolete: true

[Typedef]
id: GENO:0000783
name: has_sequence_unit
def: "A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)" []
is_a: GENO:0000654 ! has_sequence_part

[Typedef]
id: GENO:0000784
name: completely_varies_with
def: "A relation between two seqeunces or features that are considered variant with each other along their entire extents." []
is_symmetric: true
is_a: GENO:0000683 ! varies_with

[Typedef]
id: GENO:0000790
name: related_condition

[Typedef]
id: GENO:0000791
name: inferred_to_cause_condition
property_value: IAO:0000116 "Note that we currently do not have a property chain to propagate phenotypes to genes across sequence_derives_from relation (e.g. in cases where a Tg insertion derives expressed sequence from some gene)" xsd:string
property_value: IAO:0000116 "The property chains below are defined as explicitly as possible, but many could be shortened if we used the inferred_to_cause_condition property to construct the property chains.  Where this is the case, it is noted in the annotations on the property chains.\n\nBelow are the different kinds/paths of propagation we desire:\n1. Propagation 'down' a genotype (from larger components to smaller ones)\n2. Propagation 'up' a genotype (from smaller components to larger ones)\n3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype).\n4. From an effective genotype to its intrinsic and extrinsic components.\n5. From genotype components to genes (note here that a separate chain is needed to propagate conditions asserted on a sequence alteration to the gene, because of the fact that the link to the gene is from the variant locus/allele).\n6. (Exploratory). There are cases where we may also want inter-genotype propagation (i.e. propagation that extends beyond moving up or down a single genotype). For example, if a phenotype is asserted on a sex-qualified intrinsic genotype, we want it to infer down through its component sex-agnostic intrinsic genotype and then up to any effective genotypes of which this sex-agnostic intrinsic genotype is a part. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to implement a chain to support this.\n\nNote that we do not want to propagate phenotypes up from sex-agnostic genotyeps to sex-qualified ones (e.g.from shha<tbx392>/shha<tbx392> [AB] to shha<tbx392>/shha<tbx392> [AB](male)) - because it may not be the case that a phenotype assessed without consideratioon to sex will apply on a sex-specific background.  So we would not create a property chain to propagate inferred condition associations from sex-agnaostic intrinsic genotypes and their parts to sex-qualified intrinsic genotypes and effective genotypes that contain them (such as:  has_variant_part o has_sex_agnostic_part o has_variant_part o 'causes condition')" xsd:string
holds_over_chain: GENO:0000382 RO:0003303 {comment="Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype."}
holds_over_chain: GENO:0000383 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration."}
holds_over_chain: GENO:0000445 RO:0003303 {comment="Property chain to propagate inferred condition associations from a variant locus instance to a gene class (to support cases where the phenotype association is made directly at the level of the variant locus/allele)."}
holds_over_chain: GENO:0000661 RO:0003303 {comment="Property chain to propagate inferred condition associations 'down' a genotype partonomy just from a sex-qualified intrinsic genotype to the immediate sex-agnostic intrinsic genotype. (An additional property chain is needed to then propagate to the intrinsic genotype components)"}
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000793
name: inferred_to_contribute_to_condition
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000794
name: inferred_to_correlate_with_condition
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000840
name: pathogenic_for_condition
xref: LOINC:LA6668-3
is_a: RO:0003303 ! causes condition

[Typedef]
id: GENO:0000841
name: likely_pathogenic_for_condition
xref: LOINC:LA26332-9
is_a: RO:0003303 ! causes condition

[Typedef]
id: GENO:0000842
name: non-causal_for_condition
def: "Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to." []
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000843
name: benign_for_condition
xref: LOINC:LA6675-8
is_a: GENO:0000842 ! non-causal_for_condition

[Typedef]
id: GENO:0000844
name: likely_benign_for_condition
xref: LOINC:LA26334-5
is_a: GENO:0000842 ! non-causal_for_condition

[Typedef]
id: GENO:0000845
name: has_uncertain_significance_for_condition
xref: LOINC:LA26333-7
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000846
name: has_qualifying_process
def: "A relation used to describe  a process contextualizing the identity of an entity." []
is_a: GENO:0000580 ! has_qualifier

[Typedef]
id: GENO:0000847
name: has_qualifying_environment
def: "A relation used to describe  an environment contextualizing the identity of an entity." []
is_a: GENO:0000580 ! has_qualifier

[Typedef]
id: GENO:0000849
name: is_candidate_variant_for
is_a: GENO:0000790 ! related_condition

[Typedef]
id: GENO:0000903
name: has_location
def: "A relation linking a sequence feature to the location it occupies on some reference sequence." []
property_value: IAO:0000118 "occupies" xsd:string
domain: SO:0000110 ! sequence_feature
range: GENO:0000815 ! sequence feature location

[Typedef]
id: GENO:0000906
name: on strand
comment: Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from.

[Typedef]
id: GENO:0000957
name: has_defining_location
def: "Holds between a copy number complement or functional copy number complement, and a genomic location that serves as a proxy for the sequence or functional element that defines the complement." []
comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement -  by using a 'sequence location' as a proxy for a specific sequence that is found at this location.\n\nFor copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.
range: GENO:0000815 ! sequence feature location

[Typedef]
id: GENO:0000958
name: has_defining_sequence
def: "Holds between a copy number complement or functional copy number complement, and the biological sequence that defines the complement." []
comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_sequence property is used to specify the sequence defining a copy number complement.
range: GENO:0000702 ! biological sequence

[Typedef]
id: GENO:0000959
name: has_defining_feature
def: "Holds between a copy number complement or functional copy number complement and a genomic feature that serves as a proxy for the sequence that defines the complement." []
comment: Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement -  by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference.\n\nFor copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.
range: SO:0000110 ! sequence_feature

[Typedef]
id: GENO:0000966
name: has_interval
def: "Relates a sequence feature location to an interval that defines its start and end position." []
comment: Can be used when Interval objects are employed in representing sequence location.  But start and end positions can also be directly attached to a location, avoiding the use of Interval objects.
domain: GENO:0000815 ! sequence feature location

[Typedef]
id: GENO:0000967
name: has_reference_sequence
def: "Relates a  'sequence feature location' to a sequence that it is anchored to." []

[Typedef]
id: GENO:0000968
name: sequence role
def: "A role assigned to a sequence feature, collection, or genotype, e.g. serving as a 'reference' against with other  sequences are compared." []
comment: The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants.
is_a: RO:0000053 ! bearer of

[Typedef]
id: IAO:0000136
name: is about
def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." []

[Typedef]
id: IAO:0000219
name: denotes
def: "Denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" []
property_value: IAO:0000116 "Consdier if this is the best relation for linking genotypes to the genomic entities they specify.  We could use the more generic 'is about', or define a new 'specifies' relation that holds between ICEs and something it specifies the nature or creation of." xsd:string
is_a: IAO:0000136 ! is about

[Typedef]
id: OBI:0000293
name: has_specified_input
def: "A relation between a planned process and a continuant participating in that process that is not created during  the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." []
is_a: RO:0002233 ! has input

[Typedef]
id: OBI:0000299
name: has_specified_output
def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." []
is_a: RO:0002234 ! has output

[Typedef]
id: RO:0000052
name: inheres_in
def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []

[Typedef]
id: RO:0000053
name: bearer of
def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []

[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
inverse_of: RO:0000057 ! has participant

[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []

[Typedef]
id: RO:0000059
name: concretizes
def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." []
property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string

[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000087
name: has role
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0000091
name: has disposition
def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" []
is_a: RO:0000053 ! bearer of

[Typedef]
id: RO:0001000
name: derives from

[Typedef]
id: RO:0002091
name: starts during
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002093
name: ends during
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
is_symmetric: true

[Typedef]
id: RO:0002162
name: in taxon
def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []

[Typedef]
id: RO:0002200
name: has phenotype
def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." []
range: UPHENO:0001001 ! Phenotype
inverse_of: RO:0002201 ! phenotype of

[Typedef]
id: RO:0002201
name: phenotype of
domain: UPHENO:0001001 ! Phenotype

[Typedef]
id: RO:0002222
name: temporally related to

[Typedef]
id: RO:0002233
name: has input
def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
is_a: RO:0000057 ! has participant

[Typedef]
id: RO:0002234
name: has output
def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p." []
is_a: RO:0000057 ! has participant
inverse_of: RO:0002353 ! output of

[Typedef]
id: RO:0002350
name: is member of
is_a: BFO:0000050 ! is part of
inverse_of: RO:0002351 ! has member

[Typedef]
id: RO:0002351
name: has member
def: "has member is a mereological relation between a collection and an item." []
property_value: IAO:0000112 "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes\n\nExample 2: a collection of information entities such as a genotype being comprised of a background component and a variant component" xsd:string
is_a: BFO:0000051 ! has part

[Typedef]
id: RO:0002352
name: input of
is_a: RO:0000056 ! participates in

[Typedef]
id: RO:0002353
name: output of
is_a: RO:0000056 ! participates in

[Typedef]
id: RO:0002354
name: obsolete_formed as result of
is_a: ObsoleteProperty

[Typedef]
id: RO:000244
name: molecularly controls
def: "Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b" []

[Typedef]
id: RO:0002522
name: bounds sequence of
def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: GENO:0000654 ! has_sequence_part

[Typedef]
id: RO:0002524
name: has subsequence
def: "x has subsequence y iff all of the sequence parts of x are sequence parts of y" []
is_a: GENO:0000654 ! has_sequence_part
inverse_of: RO:0002525 ! is subsequence of

[Typedef]
id: RO:0002525
name: is subsequence of
is_a: GENO:0000655 ! is_sequence_part_of

[Typedef]
id: RO:0002526
name: overlaps sequence of
def: "x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y." []
property_value: http://purl.org/dc/terms/source "http://biorxiv.org/content/early/2014/06/27/006650.abstract" xsd:string
is_a: RO:0002131 ! overlaps

[Typedef]
id: RO:0002528
name: is upstream of sequence of
def: "inverse of downstream of sequence of" []

[Typedef]
id: RO:0002529
name: is downstream of sequence of
def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." []

[Typedef]
id: RO:0003301
name: is model of
def: "Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." []
comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.
property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models?  Restricted to linking biological systems and phenomena?  Inclusive of only diseases in range, or broader?" xsd:string
property_value: IAO:0000117 "Matthew Brush" xsd:string

[Typedef]
id: RO:0003302
name: causes or contributes to condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some causal or contributing role that influences the condition." []
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene  or sequence alteration.  These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology).  The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease  'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string
property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string
is_a: GENO:0000790 ! related_condition

[Typedef]
id: RO:0003303
name: causes condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has a causal role for the condition." []
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0003304
name: contributes to condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity has some contributing role in the manifestation of the condition." []
is_a: RO:0003302 ! causes or contributes to condition

[Typedef]
id: RO:0003305
name: contributes to severity of condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the severity with which a condition manifests in an individual." []
property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string
is_a: RO:0003304 ! contributes to condition

[Typedef]
id: RO:0003306
name: contributes to frequency of condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity influences the frequency of the condition in a population." []
property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string
is_a: RO:0003304 ! contributes to condition

[Typedef]
id: RO:0003307
name: is preventative for condition
def: "A relationship between an entity (a genotype, genetic variation or environment) and a condition (a phenotype or disease) where the entity prevents or reduces the severity of a condition." []
comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene  or sequence alteration.  These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology).  The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
is_a: GENO:0000790 ! related_condition

[Typedef]
id: RO:0003308
name: correlated with condition
def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." []
is_a: GENO:0000790 ! related_condition

[Typedef]
id: begin
name: begin
is_a: GENO:0000708 ! faldo properties

[Typedef]
id: end
name: end
is_a: GENO:0000708 ! faldo properties

[Typedef]
id: http://purl.org/oban/association_has_object
name: association has object

[Typedef]
id: http://purl.org/oban/association_has_predicate
name: association has predicate

[Typedef]
id: http://purl.org/oban/association_has_subject
name: association has subject

[Typedef]
id: location
name: location
is_a: GENO:0000708 ! faldo properties

[Typedef]
id: reference
name: reference (faldo)
def: "The reference is the resource that the position value is anchored to.  For example, a contig or chromosome in a genome assembly." []
is_a: GENO:0000708 ! faldo properties