GENO ontology
type: Ontology
version IRI: geno.owl
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. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013
license: https://creativecommons.org/licenses/by/4.0/
version info: 2026-02-02

is_identity_criteria
type: AnnotationProperty
definition: Used to annotation axioms that define identity criteria for instances of a class.
range: boolean

proabalistic_quantifier
type: AnnotationProperty

mixin
type: AnnotationProperty
comment: Used to flag terms that are created for organizational purposes, e.g. to support groupings useful for defining GENO-based data models.
range: boolean

gene symbol
type: AnnotationProperty

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example of usage
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred label: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

has curation status
type: AnnotationProperty
editor preferred label: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: ready for release
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
has curation status: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: OBO Operations committee
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative term

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
editor preferred label: ontology term requester
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

is denotator type
type: AnnotationProperty
editor preferred label: is denotator type
definition: Relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred label: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
term editor: Chris Mungall

expand assertion to
type: AnnotationProperty
editor preferred label: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

first order logic expression
type: AnnotationProperty
editor preferred label: first order logic expression
term editor: PERSON:Alan Ruttenberg

antisymmetric property
type: AnnotationProperty
editor preferred label: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: Use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg
sub property of: logical characteristic of object property

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred label: has ID digit count
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred label: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred label: has ID policy for
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred label: has ID prefix
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

elucidation
type: AnnotationProperty
editor preferred label: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred label: is allocated id range
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term editor: PERSON:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

has ontology root term
type: AnnotationProperty
editor preferred label: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
term editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred label: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
term editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred label: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
term editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred label: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
has curation status: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

agr_zyg
type: AnnotationProperty
definition: Set of zygosity terms for the Alliance of Genome Resources, used for AGM metadata
sub property of: SubsetProperty

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
sub property of: alternative label

database_cross_reference
type: AnnotationProperty
example of usage: disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
definition: An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
label: has cross-reference

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
sub property of: alternative label

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym
sub property of: alternative label

has related synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
sub property of: alternative label

begin
type: ObjectProperty
sub property of: faldo properties

end
type: ObjectProperty
sub property of: faldo properties

location
type: ObjectProperty
sub property of: faldo properties

reference (faldo)
type: ObjectProperty
sub property of: faldo properties
definition: The reference is the resource that the position value is anchored to. For example, a contig or chromosome in a genome assembly.

is part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of
RO_0001900: RO_0001901
label: part of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part
RO_0001900: RO_0001901

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative label: is realized by
alternative label: realized_in
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: is part of
property chain axiom: starts during
editor preferred label: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: is part of
editor preferred label: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

has_sequence_attribute
type: ObjectProperty
sub property of: topObjectProperty
domain: Class
  union of: sequence feature or set
  union of: biological sequence
  union of: qualified sequence feature or collection
definition: A relation used to link sequence entities (sequences, features, qualified features, and collections thereof) to their 'attributes'.
editor note: 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.
database_cross_reference: http://purl.obolibrary.org/obo/so_has_quality

bears_concretization_of
type: ObjectProperty
property chain axiom: bearer of
property chain axiom: concretizes
definition: 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
alternative label: materializes
comment: Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.

is_genotype_of
type: ObjectProperty
inverse of: has_genotype

has_genotype
type: ObjectProperty
domain: Class
  union of: genotype
  union of: Restriction
    on property: is part of
    some values from: genotype
definition: A relationship that holds between a biological entity and some level of genetic variation present in its genome.
editor note: This relation aims to be equally as broad/inclusive as RO:0002200 ! has_phenotype.
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.

has_proper_part
type: ObjectProperty
sub property of: has part
inverse of: is_proper_part_of
type: TransitiveProperty
definition: An antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part (source: SIO)
editor note: No proper part relation anymore in RO/BFO?
database_cross_reference: http://semanticscience.org/resource/SIO_000053

has_sequence
type: ObjectProperty
inverse of: is_sequence_of
range: biological sequence
definition: A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.
alternative label: has_sequence_component
alternative label: has_state
database_cross_reference: VMC:state
comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.

obsolete_specifies
type: ObjectProperty
sub property of: ObsoleteProperty
example of usage: A geno:intrinnsic genotype 'specifies' a SO:genome. A geno:karyotype 'specifies' a geno:karyotype feature collection.
definition: A relationship between an information content entity representing a specification, and the entity it specifies.
deprecated: true

obsolete_approximates_sequence
type: ObjectProperty
sub property of: ObsoleteProperty
editor note: 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.
deprecated: true

obsolete_resolves_to_sequence
type: ObjectProperty
sub property of: ObsoleteProperty
editor note: 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.
deprecated: true

is_proper_part_of
type: ObjectProperty
sub property of: is part of
definition: An asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.
database_cross_reference: http://semanticscience.org/resource/SIO_000093

is_sequence_of
type: ObjectProperty
domain: biological sequence

is_subject_of
type: ObjectProperty
inverse of: is about

obsolete_is_specified_by
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

obsolete_is_phenotype_of_genotype
type: ObjectProperty
sub property of: ObsoleteProperty
definition: shortcut relation used to link a phenotype directly to a genotype of an organism
alternative label: is_phenotype_of_organism_with_genotype
alternative label: is_phenotype_with_genotype
alternative label: phenotype_has_genotype
comment: Might expand to something like: phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))
deprecated: true

obsolete_participates_in_inheritance_process
type: ObjectProperty
sub property of: ObsoleteProperty
range: inheritance pattern
definition: 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.
editor note: Exploratory/temporary property, as we formalize our phenotypic inheritance model.
deprecated: true

has_variant_part
type: ObjectProperty
sub property of: has_sequence_part
inverse of: is_variant_part_of
type: TransitiveProperty
definition: 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_variant_part_of
type: ObjectProperty
sub property of: is_sequence_part_of
type: TransitiveProperty

has_reference_part
type: ObjectProperty
sub property of: has_sequence_part
inverse of: is_reference_part_of
type: TransitiveProperty
definition: A relation between a sequence entity (i.e. a sequence, feature, or qualified feature) and a part of this entity that is not variant.
alternative label: has_reference_sequence_part

is_reference_part_of
type: ObjectProperty
sub property of: is_sequence_part_of

is_allele_of
type: ObjectProperty
sub property of: has_affected_feature
inverse of: has_allele
domain: genomic feature
example of usage: <fgf8a^ti282a> is_allele_of the 'danio rerio fgf8a' gene locus.
definition: 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.
editor note: Domain = allele Range = genomic locus (but in practice it is common to use a punned gene class IRI as the subject of this relation).
editor note: 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.
alternative label: is_sequence_variant_of
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). While 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). It 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 …

obsolete_is_genetic_variant_of
type: ObjectProperty
sub property of: ObsoleteProperty
definition: 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).
alternative label: is_variant_instance_of
has obsolescence reason: formerly grouped is_allele_of and is_expression_variant_of proerpties under feature to class proeprty (now renmaed has_affected_locus)
comment: Domain = genomic feature instance Range = punned gene class IRI
deprecated: true

obsolete_has_genetic_variant
type: ObjectProperty
sub property of: ObsoleteProperty
definition: A relation linking a gene class to a sequence-varaint or expression-variant of the gene.
alternative label: has_variant_instance
has obsolescence reason: formerly grouped has_allele and has_expression_variant proerpties under cllass to feature property (now renamed locus_affected_by)
comment: Domain = punned gene class Range = genomic feature
deprecated: true

has_allele
type: ObjectProperty
sub property of: is_feature_affected_by
definition: A relation linking a gene class to one of its sequence-variant alleles.
editor note: Domain = punned gene class Range = allele
alternative label: has_sequence_variant

targets_gene
type: ObjectProperty
sub property of: has_affected_feature
inverse of: is_gene_target_of
definition: 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.

has_affected_feature
type: ObjectProperty
inverse of: is_feature_affected_by
property chain axiom: has_variant_part
property chain axiom: is_variant_part_of
definition: 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.

is_expression_variant_of
type: ObjectProperty
sub property of: has_affected_feature
inverse of: has_expression_variant
definition: A relation between an expression-variant gene (ie integrated transgenes or knockdown reagent targeted genes), and the class of gene it represents.
editor note: Domain = expression variant feature. Range = punned gene class
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.

is_feature_affected_by
type: ObjectProperty
definition: 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.
alternative label: class_to_feature_relation
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)

is_gene_target_of
type: ObjectProperty
sub property of: is_feature_affected_by
definition: A relation between a gene class and a gene targeting reagent that targets it.
alternative label: is_target_of
comment: Domain = punned gene class Range = gene knockdown reagent

has_expression_variant
type: ObjectProperty
sub property of: is_feature_affected_by
definition: A relation linking a gene class to one of an expression-variant of that gene..
editor note: Domain = punned gene class Range = expression variant feature
alternative label: has_expression_variant_instance

obsolete_is_variant_with
type: ObjectProperty
sub property of: ObsoleteProperty
definition: A relation between two sequence features at a given genomic locus that vary in their sequence or level of expression.
has obsolescence reason: Decided there was no need for a contrasting is_expression_variant_with property, so removed it and this parent grouping property.
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.
deprecated: true

obsolete_is_expression_variant_with
type: ObjectProperty
sub property of: ObsoleteProperty
definition: 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).
deprecated: true

has_qualifier
type: ObjectProperty
definition: A relation used to describe a context or conditions that define and/or identify an entity.
editor note: 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. Used in GENO to describe physical context of materialized sequence features that represent identifying criteria for instances of qualified sequence features.
alternative label: has_qualifying_context

has_zygosity
type: ObjectProperty
sub property of: has_sequence_attribute
domain: single locus complement
range: zygosity
definition: a relation to link a single locus complement to its zygosity.

is_reference_allele_of
type: ObjectProperty
sub property of: is_allele_of
domain: reference allele
definition: A relationship between a reference locus/allele and the gene class it is an allele of.

has_staining_intensity
type: ObjectProperty
sub property of: has_sequence_attribute
editor note: 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.
alternative label: has_color_value
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.

is_targeted_by
type: ObjectProperty
example of usage: Used to link a gene targeting reagent such as a morpholino, to an instance of a reagent targeted gene variant.
definition: relation between an molecular agent and its molecular target

sequence_derives_from
type: ObjectProperty
sub property of: topObjectProperty
property chain axiom: has part
example of usage: 1. Used to specify derivation of transgene components from a gene class, or a engineered construct instance. 2. 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. 3. Used to indicate derivation of a variant mouse genotype from an ES cell line used in generating the modified mice (IMPC)
definition: Relationship between a sequence feature and a distinct, non-overlapping feature from which it derives part or all of its sequence.

is_variant_allele_of
type: ObjectProperty
sub property of: is_allele_of
domain: variant allele
definition: A relationship between a variant allele and the gene class it is an allele of.

has_sex_agnostic_part
type: ObjectProperty
sub property of: has_sequence_part
inverse of: is_sex_agnostic_part_of
editor note: 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.

is_mutant_allele_of
type: ObjectProperty
sub property of: is_variant_allele_of
domain: obsolete mutant allele
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.

is_polymorphic_allele_of
type: ObjectProperty
sub property of: is_variant_allele_of
domain: polymorphic allele
definition: A relationship between a polymorphic allele and the gene class it is an allele of.

is_wild_type_allele_of
type: ObjectProperty
sub property of: is_allele_of
domain: wild-type allele
definition: A relationship between a wild-type allele and the gene class it is an allele of.

has_sequence_part
type: ObjectProperty
sub property of: has part
inverse of: is_sequence_part_of
definition: An organizational class to hold relations of parthood between sequences/features.

is_sequence_part_of
type: ObjectProperty
sub property of: is part of

is_sex_agnostic_part_of
type: ObjectProperty
sub property of: is_sequence_part_of
definition: 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.

varies_with
type: ObjectProperty
type: SymmetricProperty
definition: 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)

faldo properties
type: ObjectProperty
comment: organizational property to hold imports from faldo.

has_sequence_feature
type: ObjectProperty
domain: Class
  union of: qualified sequence feature
  union of: qualified sequence feature set
range: sequence_feature
definition: A relation linking a qualified sequence feature to its component sequence feature.
alternative label: has_sequence_feature_component
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.

has_inferred_phenotype
type: ObjectProperty
property chain axiom: has_variant_part
property chain axiom: has_asserted_phenotype
property chain axiom: is_variant_part_of
property chain axiom: is_sex_agnostic_part_of
property chain axiom: has_allele
property chain axiom: has_expression_variant

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: has_variant_part
annotated target: has_asserted_phenotype
comment: Property chain to propagate inferred phenotype associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: is_variant_part_of
annotated target: is_sex_agnostic_part_of
annotated target: has_asserted_phenotype
comment: Property chain to propagate inferred phenotype associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype.

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: is_variant_part_of
annotated target: has_asserted_phenotype
comment: Property chain to propagate inferred phenotype associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: has_allele
annotated target: is_variant_part_of
annotated target: has_asserted_phenotype
comment: Property chain to propagate inferred phenotype associations from an intrinsic genotype component (e.g. a (sequence-)variant locus instance) to a gene class.

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: has_allele
annotated target: has_asserted_phenotype
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).

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: has_expression_variant
annotated target: is_variant_part_of
annotated target: has_asserted_phenotype
comment: Property chain to propagate inferred phenotype associations from an extrinnsic genotype component (e.g. a expression-variant gene instance) to a gene class.

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: has_expression_variant
annotated target: has_asserted_phenotype
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).

Axiom
annotated source: has_inferred_phenotype
annotated property: propertyChainAxiom
annotated target: is_sex_agnostic_part_of
annotated target: has_asserted_phenotype
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)

obsolete_has_regulatory_part
type: ObjectProperty
sub property of: ObsoleteProperty
comment: Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.
deprecated: true

obsolete_is_alteration_within
type: ObjectProperty
sub property of: ObsoleteProperty
property chain axiom: is_variant_part_of
property chain axiom: is_allele_of
has curation status: exploratory term
definition: A relation linking a sequence_alteration to the gene it alters.
alternative label: is_within_allele_of
deprecated: true

has_asserted_phenotype
type: ObjectProperty
sub property of: has phenotype

is_regulatory_part_of
type: ObjectProperty
sub property of: is_sequence_part_of
editor note: Proposal for a property linking regulatory elements to larger features of which they are a part.

obsolete_has_position_component
type: ObjectProperty
sub property of: ObsoleteProperty
definition: A relation linking a sequence feature to its component Position that represents an identifying criteria for sequence feature instances.
editor note: 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.
deprecated: true

has_sequence_unit
type: ObjectProperty
sub property of: has_sequence_part
definition: A relation between a nucleic acid or amino acid sequence or sequence feature, and one of its monomeric units (nucleotide or amino acid residues)

completely_varies_with
type: ObjectProperty
sub property of: varies_with
type: SymmetricProperty
definition: A relation between two seqeunces or features that are considered variant with each other along their entire extents.

related_condition
type: ObjectProperty

inferred_to_cause_condition
type: ObjectProperty
sub property of: related_condition
property chain axiom: has_variant_part
property chain axiom: is_sex_agnostic_part_of
property chain axiom: causes condition
property chain axiom: is_variant_part_of
property chain axiom: has_allele
property chain axiom: is_feature_affected_by
editor note: 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)
editor note: 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. Below are the different kinds/paths of propagation we desire: 1. Propagation 'down' a genotype (from larger components to smaller ones) 2. Propagation 'up' a genotype (from smaller components to larger ones) 3. From sex-qualified genotypes down to the sex-agnostic genotype and its components (but not 'up' to a sex-qualified genotype). 4. From an effective genotype to its intrinsic and extrinsic components. 5. 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). 6. (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. Note 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_…

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
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)

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: has_variant_part
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
comment: This is a case of inter-gneotype phenotype propagation, requiring propagation down oen genotype and then up another. Given the data in hand, however, the conditions for this will likely never occur, so probably ok not to have this chain. This property chain propagates a phenotype asserted on a sex-qualified intrinsic genotype, down to its sex-agnostic genotype part, and then up to a parent effective genotype that has it as a variant part. I think this is OK in all cases, so we can implement this as the one case where we can have inter-genotype pheno propagation. But as noted, there will likely be no data that actually meets criteria to use this chain, so we can probably leave it out.

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: has_variant_part
annotated target: causes condition
comment: Property chain to propagate inferred condition associations 'up' a genotype partonomy in the direction of sequence alteration -> VL -> VSLC -> GVC -> genotype.

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_variant_part_of
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, to the coompnent variant parts of this sex-agnostic genotype.

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_variant_part_of
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to move past the sex-agnostic genotype and down to its parts. The following shorter chain would also suffice here: is_variant_part_of o inferred_to_cause_condition

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_variant_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations 'down' a genotype partonomy in the direction of genotype -> GVC -> VSLC -> VL -> sequence alteration.

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: has_allele
annotated target: is_variant_part_of
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype, through a sex-agnostic intrinsic genotype, through the coompnent variant parts of this sex-agnostic genotype, and to the affected gene.

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: has_allele
annotated target: is_variant_part_of
annotated target: is_sex_agnostic_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations 'down' a genotype partonomy from a sex-qualified intrinsic genotype to the components of a sex-agnostic intrinsic genotype. This chain in particuular is needed to get the conditions to propagate to genes. The shorter chain below would also suffice for this propagation: has_allele o inferred_to_cause_condition

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_feature_affected_by
annotated target: has_variant_part
annotated target: causes condition
comment: Property chain to propagate inferred condition associations from an sequence alteration through the variant locus to a gene class. (separate chains are needed to propagate from the variant locus to the gene class, and another to propagate from a genotype, GVC, or VSLC to the gene class). NOTE that i dont need this property chain if I have a property chain to infer a has_affected_locus link from a sequence alteration to a gene when the link is asserted from the variant locus to the gene: is_variant_part_of o has_affected_locus --> has_affected_locus

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_feature_affected_by
annotated target: is_variant_part_of
annotated target: causes condition
comment: Obsolete comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GC, or VLSC to a gene class. (a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class). The following, shorter chain, would also suffice here: has_allele o inferred_to_cause_condition -> inferred_to_cause_condition
comment: Property chain to propagate inferred condition associations from an intrinsic genotype, GVC, or VLSC to an affected gene class, or from an extrinsic gneotype or component to an affected gene class. The following, shorter chain, would also suffice here: has_affected_locus o inferred_to_cause_condition -> inferred_to_cause_condition Note that a separate chain is needed to propagate from the variant locus to the gene class, and another to propagate from a sequence alteration to the gene class in cases where the link to gene is through the variant locus rather than the seq alteration).

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_feature_affected_by
annotated target: causes condition
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).

Axiom
annotated source: inferred_to_cause_condition
annotated property: propertyChainAxiom
annotated target: is_sex_agnostic_part_of
annotated target: is_variant_part_of
annotated target: causes condition
comment: Property chain to propagate inferred condition associations from an effective genotype through a sex-qualified intrinsic genotype to a sex-agnostic intrinsic genotype.

inferred_to_contribute_to_condition
type: ObjectProperty
sub property of: related_condition

inferred_to_correlate_with_condition
type: ObjectProperty
sub property of: related_condition

pathogenic_for_condition
type: ObjectProperty
sub property of: causes condition
database_cross_reference: LOINC:LA6668-3

likely_pathogenic_for_condition
type: ObjectProperty
sub property of: causes condition
database_cross_reference: LOINC:LA26332-9

non-causal_for_condition
type: ObjectProperty
sub property of: related_condition
definition: Relation between an entity and a condition (disease, phenotype) which it does not cause or contribute to.

benign_for_condition
type: ObjectProperty
sub property of: non-causal_for_condition
database_cross_reference: LOINC:LA6675-8

likely_benign_for_condition
type: ObjectProperty
sub property of: non-causal_for_condition
database_cross_reference: LOINC:LA26334-5

has_uncertain_significance_for_condition
type: ObjectProperty
sub property of: related_condition
database_cross_reference: LOINC:LA26333-7

has_qualifying_process
type: ObjectProperty
sub property of: has_qualifier
definition: A relation used to describe a process contextualizing the identity of an entity.

has_qualifying_environment
type: ObjectProperty
sub property of: has_qualifier
definition: A relation used to describe an environment contextualizing the identity of an entity.

is_candidate_variant_for
type: ObjectProperty
sub property of: related_condition

has_location
type: ObjectProperty
domain: sequence_feature
range: sequence feature location
definition: A relation linking a sequence feature to the location it occupies on some reference sequence.
alternative label: occupies

on strand
type: ObjectProperty
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.

has_defining_location
type: ObjectProperty
domain: Class
  union of: copy number complement
  union of: functional copy complement
range: sequence feature location
definition: 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. For 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.

has_defining_sequence
type: ObjectProperty
domain: Class
  union of: copy number complement
  union of: functional copy complement
range: biological sequence
definition: 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.

has_defining_feature
type: ObjectProperty
domain: Class
  union of: copy number complement
  union of: functional copy complement
range: sequence_feature
definition: 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. For 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.

has_interval
type: ObjectProperty
domain: sequence feature location
definition: 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.

has_reference_sequence
type: ObjectProperty
definition: Relates a 'sequence feature location' to a sequence that it is anchored to.

sequence role
type: ObjectProperty
sub property of: bearer of
definition: 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 about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition: 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
definition: 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
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
editor note: 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.
term editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan

denoted by
type: ObjectProperty
domain: entity
range: information content entity
definition: inverse of the relation 'denotes'
term editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
sub property of: has input
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: 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.
definition: The inverse property of is_specified_input_of
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: ready for release
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
sub property of: has output
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: ready for release
definition: 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.
definition: The inverse property of is_specified_output_of
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: ready for release
definition: 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.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: metadata complete
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI

inheres_in
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this fragility is a characteristic of this vase
example of usage: this red color inheres in this apple
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
definition: 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
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative label: inheres_in
RO_0001900: RO_0001901
label: characteristic of
label: inheres in

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
definition: 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
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901
label: has characteristic

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
example of usage: 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 journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
definition: A relationship between a generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
domain: Class
  union of: process
  union of: specifically dependent continuant
range: generically dependent continuant
example of usage: 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).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: 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.
definition: A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.

function of
type: ObjectProperty
sub property of: inheres_in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of

quality of
type: ObjectProperty
sub property of: inheres_in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative label: is quality of
alternative label: quality_of

role of
type: ObjectProperty
sub property of: inheres_in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative label: is role of
alternative label: role_of

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative label: has_role

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: inheres_in
definition: inverse of has disposition

derives from
type: ObjectProperty
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative label: derives_from
imported from: ro.owl

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative label: derives_into

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.

has component activity
type: ObjectProperty
sub property of: has component process

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

during which ends
type: ObjectProperty
sub property of: temporal relation
inverse of: ends during
term editor: https://orcid.org/0000-0002-7073-9172

ends after
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
term editor: https://orcid.org/0000-0002-7073-9172

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: starts_at_end_of

during which starts
type: ObjectProperty
sub property of: temporal relation
inverse of: starts during
term editor: https://orcid.org/0000-0002-7073-9172

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: ends_at_start_of
alternative label: meets

starts during
type: ObjectProperty
sub property of: temporal relation
domain: occurrent
range: occurrent
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: io

ends during
type: ObjectProperty
sub property of: temporal relation
term editor: https://orcid.org/0000-0002-7073-9172
alternative label: o
alternative label: overlaps

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: is part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism
property chain axiom: overlaps
property chain axiom: regulates
property chain axiom: capable of
property chain axiom: has developmental contribution from
property chain axiom: results in developmental progression of
property chain axiom: has potential to develop into
has curation status: pending final vetting
definition: 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.
term editor: 0000-0001-9227-417X
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
has_narrow_synonym: life cycle stage of

has component
type: ObjectProperty
sub property of: has part
has curation status: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.

has phenotype
type: ObjectProperty
sub property of: has phenotype or disease
inverse of: phenotype of
domain: Class
  union of: generically dependent continuant
  union of: disease
  union of: material anatomical entity
range: Phenotype
has curation status: pending final vetting
definition: 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).
term editor: https://orcid.org/0000-0002-6601-2165

phenotype of
type: ObjectProperty
type: FunctionalProperty
domain: Phenotype
has curation status: pending final vetting
definition: inverse of has phenotype
term editor: https://orcid.org/0000-0002-6601-2165

develops from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
term editor: https://orcid.org/0000-0001-9114-8737
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
has curation status: pending final vetting
definition: inverse of develops from
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0002-7073-9172
term editor: https://orcid.org/0000-0003-1980-3228

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
term editor: https://orcid.org/0000-0001-7476-6306
term editor: https://orcid.org/0000-0002-3837-8864
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
definition source: GO
elucidation: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in

temporal relation
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
editor note: move to BFO?
term editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
definition source: Allen
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
label: temporally related to

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
has curation status: pending final vetting
definition: 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.
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: consumes

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
has curation status: pending final vetting
definition: 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.
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: produces

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
example of usage: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
has curation status: pending final vetting
definition: x has developmental contribution from y iff x has some part z such that z develops from y
term editor: https://orcid.org/0000-0002-6601-2165

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: is part of
has curation status: pending final vetting
definition: inverse of has developmental contribution from
term editor: https://orcid.org/0000-0002-6601-2165

developmentally preceded by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
has curation status: pending final vetting
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
editor note: false
term editor: https://orcid.org/0000-0002-6601-2165

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: pending final vetting
definition: Inverse of developmentally preceded by
term editor: https://orcid.org/0000-0002-6601-2165

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: biological_process
range: anatomical entity
has curation status: pending final vetting
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
editor note: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
term editor: https://orcid.org/0000-0002-6601-2165

results in formation of anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
example of usage: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
has curation status: pending final vetting
term editor: https://orcid.org/0000-0002-6601-2165
definition source: GOC:mtg_berkeley_2013

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: is part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process
term editor: https://orcid.org/0000-0002-6601-2165

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: https://orcid.org/0000-0002-6601-2165

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
term editor: https://orcid.org/0000-0002-6601-2165

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
term editor: https://orcid.org/0000-0002-6601-2165

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: false

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: is part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: actively involved in
alternative label: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
term editor: https://orcid.org/0000-0002-6601-2165

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
term editor: https://orcid.org/0000-0002-6601-2165

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
term editor: https://orcid.org/0000-0002-6601-2165

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
term editor: https://orcid.org/0000-0002-6601-2165

is member of
type: ObjectProperty
sub property of: is part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative label: is member of
alternative label: member part of
definition source: SIO
RO_0001900: RO_0001901
label: member of

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
example of usage: Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
RO_0001900: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
term editor: https://orcid.org/0000-0002-6601-2165

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
term editor: https://orcid.org/0000-0002-6601-2165

formed as result of
type: ObjectProperty
sub property of: output of
sub property of: ObsoleteProperty
term editor: https://orcid.org/0000-0002-6601-2165
label: obsolete_formed as result of

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
has curation status: requires discussion
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
term editor: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
term editor: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
term editor: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
has curation status: requires discussion
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
term editor: https://orcid.org/0000-0002-6601-2165

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: requires discussion
definition: inverse of upstream of
term editor: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
term editor: https://orcid.org/0000-0002-6601-2165

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly activates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly inhibits

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
term editor: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
term editor: https://orcid.org/0000-0002-6601-2165

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
term editor: https://orcid.org/0000-0002-6601-2165

provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: has output
property chain axiom: has input
definition: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: directly provides input for
definition source: causal-relations

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of or within, positive effect
type: TransitiveProperty
domain: process
range: process
has curation status: requires discussion
definition: transitive form of directly_provides_input_for
term editor: https://orcid.org/0000-0002-6601-2165

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: is part of
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
term editor: https://orcid.org/0000-0002-6601-2165

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: involved in or reguates

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
editor note: Considering relabeling as 'pairwise interacts with'
term editor: https://orcid.org/0000-0002-6601-2165

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: binds
alternative label: molecularly binds with

molecularly controls
type: ObjectProperty
definition: Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly inhibits

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly activates

helper property (not for use in curation)
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

depends on
type: ObjectProperty
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

sequentially related to
type: ObjectProperty
domain: sequentially ordered entity
range: sequentially ordered entity
definition: A relation that holds between two entities that have the property of being sequences or having sequences.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

bounds sequence of
type: ObjectProperty
sub property of: has_sequence_part
sub property of: sequentially related to
inverse of: is bound by sequence of
type: TransitiveProperty
example of usage: The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)
definition: 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
term editor: https://orcid.org/0000-0002-6601-2165
term editor: Chris Mungall

is bound by sequence of
type: ObjectProperty
sub property of: sequentially related to
type: TransitiveProperty
definition: inverse of bounds sequence of
term editor: https://orcid.org/0000-0002-6601-2165

has subsequence
type: ObjectProperty
sub property of: has part
sub property of: has_sequence_part
sub property of: bounds sequence of
sub property of: overlaps sequence of
inverse of: is subsequence of
type: TransitiveProperty
definition: x has subsequence y iff all of the sequence parts of x are sequence parts of y
definition: x has subsequence y iff all of the sequence parts of y are sequence parts of x
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: contains
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20226267

is subsequence of
type: ObjectProperty
sub property of: is part of
sub property of: is_sequence_part_of
sub property of: is bound by sequence of
sub property of: overlaps sequence of
type: TransitiveProperty
definition: inverse of has subsequence
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: contained by

overlaps sequence of
type: ObjectProperty
sub property of: overlaps
sub property of: sequentially related to
type: SymmetricProperty
property chain axiom: has subsequence
property chain axiom: is subsequence of
definition: x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y.
definition: x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.
term editor: https://orcid.org/0000-0002-6601-2165
source: http://biorxiv.org/content/early/2014/06/27/006650.abstract

does not overlap sequence of
type: ObjectProperty
sub property of: sequentially related to
type: SymmetricProperty
definition: x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.
term editor: https://orcid.org/0000-0002-6601-2165
alternative label: disconnected from

is upstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: inverse of downstream of sequence of
term editor: https://orcid.org/0000-0002-6601-2165

is downstream of sequence of
type: ObjectProperty
sub property of: does not overlap sequence of
type: TransitiveProperty
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
term editor: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
term editor: https://orcid.org/0000-0002-6601-2165

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
term editor: https://orcid.org/0000-0002-6601-2165
term editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
term editor: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
term editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

correlated with
type: ObjectProperty
definition: A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.

has model
type: ObjectProperty
inverse of: has role in modeling
definition: Inverse of is-model-of

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
definition source: causal-relations

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
definition source: causal-relations

has role in modeling
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.
definition: 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.
editor note: 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?
term editor: https://orcid.org/0000-0002-1048-5019
term editor: Matthew Brush
alternative label: is used to study
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.
label: is model of

causes or contributes to condition
type: ObjectProperty
sub property of: related_condition
sub property of: causally related to
example of usage: The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
editor note: 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'.
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. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.

causes condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.

contributes to condition
type: ObjectProperty
sub property of: causes or contributes to condition
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.

contributes to severity of condition
type: ObjectProperty
sub property of: contributes to condition
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
alternative label: contributes to expressivity of condition

contributes to frequency of condition
type: ObjectProperty
sub property of: contributes to condition
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
alternative label: contributes to penetrance of condition

ameliorates condition
type: ObjectProperty
sub property of: related_condition
sub property of: contributes to severity of condition
definition: 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.
definition: A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
alternative label: is preventative for 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. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.
label: is preventative for condition

correlated with condition
type: ObjectProperty
sub property of: related_condition
sub property of: correlated with
definition: A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: inheres_in
property chain axiom: is concretized as
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
definition source: [072-ISO]

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: bearer of
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
definition source: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
term editor: https://orcid.org/0000-0003-4639-4431

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

has phenotype or disease
type: ObjectProperty

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
example of usage: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.

is anatomical entity
type: ObjectProperty
domain: anatomical entity
definition: This property only applies to anatomical entities.

association has object
type: ObjectProperty

association has predicate
type: ObjectProperty

association has subject
type: ObjectProperty

position
type: DatatypeProperty
comment: The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is.

has_extent
type: DatatypeProperty
range: int
definition: Property linking a sequence or sequence feature to an integer representing its length in terms of the number of units in the sequence.

has_sequence_string
type: DatatypeProperty
domain: sequence_feature
range: string
definition: Shortcut relation linking a sequence feature directly to a string representing the 'state' of its sequence - i.e. the ordering of units that comprise it (e.g. 'atgcagctagctaccgtcgatcg').

ObsoleteDataProperty
type: DatatypeProperty
deprecated: true

has_quantifier
type: DatatypeProperty
example of usage: The 'rank' quantifier in Bgee gene-anatomy associations, that indicates the imporatnace/specificity of a gene expression in a given anatommy relative to expressionin other anatomies for the same gene.
definition: Property to link an assertion or association with some value quantifying its relevance or ranking.

start_position
type: DatatypeProperty
definition: The starting position of a sequence feature or interval.

end_position
type: DatatypeProperty
definition: The ending position of a sequence feature or interval.

has_string
type: DatatypeProperty
domain: biological sequence
range: string
definition: Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').

has_member_count
type: DatatypeProperty
definition: Describes the number of members in some set.
alternative label: has_count
comment: In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.

Both strands
type: Class
subclass of: Stranded position

Exact position
type: Class
subclass of: Position
definition: A position that is exactly known.

Positive strand
type: Class
subclass of: Stranded position

Position
type: Class
subclass of: genomic feature location
definition: Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.
editor note: 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).
imported from: FALDO

Region
type: Class
subclass of: sequence_feature
subclass of: Class
  intersection of: Restriction
    on property: begin
    qualified cardinality: 1
    on class: Position
  intersection of: Restriction
    on property: end
    qualified cardinality: 1
    on class: Position
subclass of: Restriction
  on property: begin
  some values from: Position
subclass of: Restriction
  on property: end
  some values from: Position
definition: 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.
editor note: 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.

Negative strand
type: Class
subclass of: Stranded position

Stranded position
type: Class
subclass of: 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'.

software development
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      union of: software
      union of: source code module
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: software
    union of: source code module
definition: A planned process that has specified output a software product and that involves the creation of source code.
term editor: Mathias Brochhausen
term editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Software_development
elucidation: A planned process resulting in a software product involving the creation of source code.

dataset creating
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: data set
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data set
editor preferred label: creating a data set
definition: A planned process that has a data set as its specified output.
term editor: William R. Hogan
alternative label: data set creation
alternative label: dataset creation

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: is part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: is part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: Continuant
editor preferred label: continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: 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
editor note: 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
imported from: pato.owl
elucidation: 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])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: is part of
  all values from: occurrent
disjoint with: Restriction
  on property: is part of
  some values from: continuant
BFO_0000179: occurrent
BFO_0000180: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: is part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

process
type: Class
subclass of: occurrent
BFO_0000179: process
BFO_0000180: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO_0000179: disposition
BFO_0000180: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocitosis and exocitosis
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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
editor note: 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.
elucidation: 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])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: is part of
  all values from: realizable entity
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
elucidation: 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])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: is part of
  all values from: quality
BFO_0000179: quality
BFO_0000180: Quality
editor preferred label: quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: pato.owl
elucidation: 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])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: is part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
editor preferred label: specifically dependent continuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: 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])
definition: 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])
editor note: 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.
imported from: pato.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO_0000179: role
BFO_0000180: Role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: 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.
elucidation: b is a role means: b is a realizable entity & 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& 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])
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & 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& 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: is part of
  all values from: generically dependent continuant
BFO_0000179: gdc
BFO_0000180: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: 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])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
BFO_0000179: material
BFO_0000180: MaterialEntity
editor preferred label: material entity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
imported from: cl.owl
imported from: ido.owl
imported from: uberon.owl
elucidation: 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])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: Stub class to serve as root of hierarchy for imports of molecular entities from ChEBI ontology.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative label: polymer
imported from: chebi.owl

cell line cell
type: Class
subclass of: secondary cultured cell
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell line
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell line
editor preferred label: cell line cell
editor preferred label: 细胞系细胞 @zh
definition: A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
definition: 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分
imported from: clo.owl
label: 细胞系细胞 @zh

cell line
type: Class
subclass of: organismal entity
subclass of: secondary cultured cell population
subclass of: Restriction
  on property: has grain
  some values from: cell line cell
subclass of: Restriction
  on property: derives from
  some values from: organism
subclass of: Restriction
  on property: has grain
  all values from: cell line cell
editor preferred label: cell line
editor preferred label: 细胞系 @zh
definition: 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).
definition: 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 @zh
definition: 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。
imported from: clo.owl
label: 细胞系 @zh

cell
type: Class
subclass of: anatomical structure
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
editor note: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
editor note: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
imported from: cl.owl
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: MESH:D002477
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
comment: Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.

Axiom
annotated source: cell
annotated property: definition
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
database_cross_reference: CARO:mah

primary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  complement of: Restriction
    on property: is_specified_output_of
    some values from: cell culture splitting
subclass of: Class
  complement of: Restriction
    on property: derives from
    some values from: Class
      intersection of: cultured cell
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: cell culture splitting
editor preferred label: primary cultured cell
definition: A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
imported from: cl.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl

B cell
type: Class
subclass of: lymphocyte
editor preferred label: B cell
definition: A lymphocyte of B lineage that is capable of B cell mediated immunity.
imported from: cl.owl

lymphocyte
type: Class
subclass of: mononuclear cell
editor preferred label: lymphocyte
definition: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
imported from: cl.owl

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl

mononuclear cell
type: Class
subclass of: cell
editor preferred label: mononuclear cell
definition: A leukocyte with a single non-segmented nucleus in the mature form.
imported from: cl.owl

environmental system
type: Class
subclass of: system
definition: A system which has the disposition to environ one or more material entities.
editor note: 1. Stub class to serve as root of hierarchy for imports from an ontology of environment and experimental conditions. 2. 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).
database_cross_reference: EcoLexicon:environment
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.

Axiom
annotated source: environmental system
annotated property: definition
annotated target: A system which has the disposition to environ one or more material entities.
database_cross_reference: DOI:10.1186/2041-1480-4-43

genomic genotype (sex-agnostic)
type: Class
subclass of: genomic genotype
example of usage: Example zebrafish intrinsic genotype: Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) reference component (genomic background) = AB variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> . . . and within this variant component, there are two 'variant single locus complements' represented: allele complement 1 = fgf8a<ti282a/+> allele complement 2 = shha<tb392/tb392> and within each of these 'variant single locus complements' there is one or more variant gene locus member: in complement 1: fgf8a<ti282a> in complement 2: shha<ttb392>
definition: 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)
editor note: 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). Conceptually, 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.
alternative label: genotype
alternative label: organismal genotype
alternative label: sex-agnostic intrinsic genotype
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).

variant allele
type: Class
equivalent class: Class
  intersection of: allele
  intersection of: Restriction
    on property: varies_with
    some values from: reference allele
subclass of: allele
subclass of: Class
  union of: sequence_alteration
  union of: Restriction
    on property: has subsequence
    some values from: sequence_alteration
subclass of: Restriction
  on property: varies_with
  some values from: reference allele
definition: An allele that varies in it sequence from what is considered the reference or canonical sequence at that location.
editor note: 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.
alternative label: alternate allele
alternative label: sequence-variant feature
alternative label: variant feature
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. A 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.

genomic variation complement
type: Class
equivalent class: Class
  intersection of: genomic feature set
  intersection of: Restriction
    on property: has_variant_part
    some values from: variant single locus complement
subclass of: genomic feature set
subclass of: Restriction
  on property: has_variant_part
  some values from: variant single locus complement
definition: A genomic feature set representing all 'variant single locus complements' in a single genome, which together constitute the 'variant' component of a genomic genotype.
editor note: 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.
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. In model organisms, the majority of genotypes describe variation at a single location in the genome (ie only one 'single-locus variant complement') that are variant realtive to some reference background. For example, the genotype instance 'fgf8a<t1282a/+>(AB)') exhibits a mutation at only one locus. But some genotypes describe variation at more than one location (e.g. a double mutant that has alterations in the fgf8a gene and the shh gene)).

background genome
type: Class
subclass of: reference genome
example of usage: The ZFIN background 'AB' that serves as a reference as part of the genotype fgf8a^ti282a/+ (AB)
definition: A reference genome that represents the sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).
editor note: 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.
alternative label: genomic background
database_cross_reference: OBI:genetic population background information

gene allele
type: Class
subclass of: allele
subclass of: Restriction
  on property: is_allele_of
  some values from: gene
example of usage: 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. http://useast.ensembl.org/Danio_rerio/Gene/Summary?g=ENSDARG00000056722 https://zfin.org/ZDB-ALT-111117-8
definition: 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)
editor note: 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). This 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.
database_cross_reference: http://purl.obolibrary.org/obo/SO_0001023 ! allele
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. A 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.

reference sequence
type: Class
equivalent class: Class
  intersection of: biological sequence
  intersection of: Restriction
    on property: sequence role
    some values from: reference
subclass of: biological sequence
subclass of: Restriction
  on property: sequence role
  some values from: reference
definition: A sequence that serves as a standard against which other sequences at the same location are compared.
editor note: 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.
alternative label: reference sequence
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.

obsolete sequence feature collection
type: Class
definition: a collection more than one sequence features (ie a collection of discontinuous sequence features)
database_cross_reference: 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)
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.
deprecated: true

obsolete genomic feature collection
type: Class
definition: A sequence feature collection comprised of discontiguous sequences from a single genome
editor note: 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.
alternative label: genomic feature collection
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.
deprecated: true

obsolete reference single locus complement
type: Class
definition: A single locus complement that serves as a standard against which 'variant' sequences are compared
alternative label: reference allelic complement
alternative label: reference single locus feature complement
has obsolescence reason: Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. Eq Class axiom: 'single locus complement' and (has_sequence_attribute some reference) SC axioms: 'has member' exactly 0 'variant allele' 'has member' only 'reference genomic feature' 'has member' some 'reference genomic feature'
deprecated: true

variant single locus complement
type: Class
equivalent class: Class
  intersection of: single locus complement
  intersection of: Restriction
    on property: has_variant_part
    some values from: variant allele
subclass of: single locus complement
subclass of: Restriction
  on property: has_variant_part
  some values from: variant allele
definition: 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).
alternative label: variant allelic complement
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. Note 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.

variant genome
type: Class
equivalent class: Class
  intersection of: genome
  intersection of: Restriction
    on property: varies_with
    some values from: reference genome
subclass of: genome
subclass of: Restriction
  on property: has_variant_part
  some values from: sequence_alteration
subclass of: Restriction
  on property: varies_with
  some values from: reference genome
definition: A genome that varies at one or more loci from the sequence of some reference genome.
database_cross_reference: 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)

reference allele
type: Class
equivalent class: Class
  intersection of: allele
  intersection of: Restriction
    on property: sequence role
    some values from: reference
subclass of: allele
subclass of: Restriction
  on property: sequence role
  some values from: reference
definition: 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. In 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.

obsolete unspecified feature
type: Class
has curation status: exploratory term
definition: A genomic feature known to exist, but remaining uncharacterized with respect to its identity (e.g. which allele exists at a given gene locus).
editor note: 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 ' /? '.
has obsolescence reason: Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. Eq Class def: 'genomic feature' and (has_sequence_attribute some unspecified)
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).
deprecated: true

obsolete reference junction
type: Class
definition: 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.
alternative label: hemizygous reference junction
has obsolescence reason: Eliminating unecessary defined/organizational classes. Former logical def: junction and (has_sequence_attribute some reference) Subclass axiom: is_variant_with some insertion
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. The 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.
deprecated: true

danio rerio gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: in taxon
    some values from: Danio rerio
subclass of: gene
subclass of: Restriction
  on property: in taxon
  some values from: Danio rerio
definition: A gene that originates from the genome of a danio rerio.

homo sapiens gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: in taxon
    some values from: Homo sapiens
subclass of: gene
subclass of: Restriction
  on property: in taxon
  some values from: Homo sapiens
definition: A gene that originates from the genome of a homo sapiens.

mus musculus gene
type: Class
equivalent class: Class
  intersection of: gene
  intersection of: Restriction
    on property: in taxon
    some values from: Mus musculus
subclass of: gene
subclass of: Restriction
  on property: in taxon
  some values from: Mus musculus
definition: A gene that originates from the genome of a mus musculus.

obsolete reference gene allele
type: Class
example of usage: 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. http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164690 Note 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
definition: A version/allele of a gene that serves as a standard against which variant genes are compared.
alternative label: reference gene
has obsolescence reason: Not required at present for any specific use case, so marking as exploratory and obsoleting for simplicity. Eq Class axiom: 'gene allele' and (has_sequence_attribute some reference) SC axioms: is_variant_with some 'gene allele' is_reference_allele_of some gene
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. In 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.
deprecated: true

obsolete experimental insertion
type: Class
deprecated: true

gene trap insertion
type: Class
subclass of: insertion

integrated transgene
type: Class
subclass of: transgene
subclass of: Restriction
  on property: is part of
  some values from: transgenic_insertion
definition: 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. An '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.

genomic material
type: Class
subclass of: genetic material
subclass of: Restriction
  on property: has disposition
  some values from: heritable
has curation status: exploratory term
definition: 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.
editor note: 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. 2. 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.
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. 2. 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.

material genome
type: Class
subclass of: material entity
definition: 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.
alternative label: physical genome
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. 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/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome.

human population
type: Class
subclass of: population
definition: a population of homo sapiens grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role)
editor note: Consider http://semanticscience.org/resource/SIO_001062 ! human population ("A human population refers to a collection of human beings").
alternative label: homo sapiens population

strain or breed
type: Class
subclass of: taxonomic group
subclass of: Restriction
  on property: in taxon
  some values from: organism
definition: A maximal collection of organisms of a single species that have been bred or experimentally manipulated with the goal of being genetically identical.
alternative label: organism strain or breed
comment: Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)

taxonomic group
type: Class
subclass of: collection of organisms
editor note: 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)

mus musculus strain
type: Class
subclass of: strain or breed

danio rerio strain
type: Class
subclass of: strain or breed
subclass of: Restriction
  on property: has member
  some values from: Danio rerio
subclass of: Restriction
  on property: has member
  all values from: Danio rerio

obsolete sequence feature collection attribute
type: Class
definition: sequence attribute that can inhere only in a collection of more than one sequence features
deprecated: true

in cis
type: Class
subclass of: allelic phase
definition: A quality inhering in a collection of discontinuous sequence features in a single genome that reside on the same macromolecule (eg the same chromosomes).

in trans
type: Class
subclass of: allelic phase
definition: A quality inhering in a collection of discontinuous sequence features in a single genome that reside on different macromolecules (e.g. different chromosomes).

zygosity
type: Class
subclass of: allelic state
subclass of: Restriction
  on property: inheres_in
  some values from: single locus complement
definition: 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).
alternative label: allelic state
definition source: derived from https://en.wikipedia.org/wiki/Zygosity
database_cross_reference: http://semanticscience.org/resource/SIO_001263

hemizygous
type: Class
subclass of: disomic zygosity
definition: 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)
in subset: agr_zyg

heterozygous
type: Class
subclass of: disomic zygosity
definition: 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).
in subset: agr_zyg

homozygous
type: Class
subclass of: disomic zygosity
definition: 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).
in subset: agr_zyg

unspecified zygosity
type: Class
subclass of: zygosity
alternative label: indeterminite zygosity
alternative label: no-call zygosity
alternative label: unknown zygosity
in subset: agr_zyg

Axiom
annotated source: unspecified zygosity
annotated property: alternative label
annotated target: indeterminite zygosity
comment: MGI uses this term when zygosity is not known.

Axiom
annotated source: unspecified zygosity
annotated property: alternative label
annotated target: no-call zygosity
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)

heritabililty
type: Class
subclass of: disposition
definition: 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). We 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.

heritable
type: Class
subclass of: heritabililty

non-heritable
type: Class
subclass of: heritabililty

inheritance pattern
type: Class
subclass of: disposition
definition: 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.
editor note: 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.
alternative label: mode of inheritance
alternative label: phenotypic inheritance pattern
database_cross_reference: http://purl.obolibrary.org/obo/HP_0000005
database_cross_reference: http://purl.obolibrary.org/obo/NCIT_C45827
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. These 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.

obsolete dominant inheritance
type: Class
definition: 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
has obsolescence reason: Triage until decide if want to define this as grouping class that would result in multiple-inheritance.
deprecated: true

co-dominant autosomal inheritance
type: Class
subclass of: autosomal dominant inheritance
definition: An autosomal dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.

complete autosomal dominant inheritance
type: Class
subclass of: autosomal dominant inheritance
definition: 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.
alternative label: pure dominant inheritance

incomplete autosomal dominant inheritance
type: Class
subclass of: autosomal dominant inheritance
definition: 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.
alternative label: intermediate dominant autosomal inheritance
alternative label: semi-dominant autosomal inheritance

X-linked dominant inheritance
type: Class
subclass of: X-linked inheritance
definition: An X-linked inheritance pattern wherein the trait manifests in heterozygotes.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001423

autosomal dominant inheritance
type: Class
subclass of: autosomal inheritance
definition: An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in heterozygotes.
alternative label: vertical inheritance
database_cross_reference: http://purl.obolibrary.org/obo/HP_0000006

autosomal recessive inheritance
type: Class
subclass of: autosomal inheritance
definition: An inheritance pattern wherein a trait caused by alleles of an autosomal gene manifests in homozygous but not heterozygote individuals.

X-linked recessive inheritance
type: Class
subclass of: X-linked inheritance
definition: 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.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001419

obsolete autosomal recessive inheritance
type: Class
has obsolescence reason: duplicate term, use GENO:0000148
deprecated: true

reference
type: Class
subclass of: variation attribute
definition: 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.

unspecified life cycle stage
type: Class
subclass of: life cycle stage

obsolete genetic insertion technique
type: Class
deprecated: true

obsolete mutagen treatment technique
type: Class
deprecated: true

obsolete targeted gene mutation technique
type: Class
deprecated: true

obsolete random genetic insertion technique
type: Class
deprecated: true

obsolete targeted genetic insertion technique
type: Class
deprecated: true

obsolete enhancer trapping technique
type: Class
deprecated: true

obsolete gene trapping technique
type: Class
deprecated: true

obsolete promoter trapping technique
type: Class
deprecated: true

obsolete targeted knock-in technique
type: Class
deprecated: true

obsolete random transgene insertion technique
type: Class
deprecated: true

obsolete chromosome complement
type: Class
definition: A single locus complement that represents the collection of all chromosome sequences for a given chromosome in a single genome
deprecated: true

gained aneusomic chromosome
type: Class
subclass of: aneusomic chromosome
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: novel
has curation status: exploratory term
definition: A complete chromosome that has been abnormally duplicated in a genome, typically as the result of a meiotic non-disjunction event or unbalanced translocation
alternative label: duplicate chromosome
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.

lost aneusomic chromosome
type: Class
subclass of: aneusomic chromosome
subclass of: Restriction
  on property: has_extent
  has value: 0
has curation status: exploratory term
definition: A 'deletion' resulting from the loss of a complete chromosome, typically as the result of a meiotic non-disjunction event or unbalanced translocation.
editor note: 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".
alternative label: absent aneusomic chromosome

aneusomic chromosomal part
type: Class
subclass of: chromosome part
subclass of: sequence_alteration
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: aneusomic
has curation status: exploratory term
definition: A large deletion or terminal addition of part of some non-homologous chromsosome, as the result of an unbalanced translocation.
editor note: 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.
alternative label: aneuploid chromosomal segment
alternative label: aneusomic chromosomal subregion/segment
alternative label: partial aneusomic chromosomal element
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."

gained aneusomic chromosomal segment
type: Class
subclass of: aneusomic chromosomal part
has curation status: exploratory term
definition: A part of some non-homologous chromosome that has been gained as the result of an unbalanced translocation event.
alternative label: duplicate partial aneuploid chromosomal element
alternative label: translocated duplicate chromosomal element
alternative label: translocated duplicate chromosomal segment
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.

lost aneusomic chromosomal segment
type: Class
subclass of: aneusomic chromosomal part
subclass of: Restriction
  on property: has_extent
  has value: 0
has curation status: exploratory term
definition: A deletion of a terminal portion of a chromosome resulting from an unbalanced translocation to another chromosome.
editor note: In our model, we consider this chromosomal region to be monosomic, and thus a variant single locus complement
alternative label: dropped partial anneuploid chromosomal element
alternative label: translocated absent chromosomal segment
alternative label: truncated chromosome terminus
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. Loss 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.

aneusomic chromosome
type: Class
subclass of: chromosome
subclass of: sequence_alteration
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: aneusomic
has curation status: exploratory term
definition: 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
alternative label: complete aneusomic chromosome
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. Similarly, 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.

biological process
type: Class
subclass of: process
editor note: Stub class to serve as root of hierarchy for imports of biological processes from GO-BP.

disomic zygosity
type: Class
subclass of: zygosity
definition: 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).
in subset: agr_zyg

aneusomic zygosity
type: Class
subclass of: zygosity
definition: 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).
in subset: agr_zyg

trisomic homozygous
type: Class
subclass of: aneusomic zygosity
in subset: agr_zyg

trisomic heterozygous
type: Class
subclass of: aneusomic zygosity
in subset: agr_zyg

compound heterozygous
type: Class
subclass of: heterozygous
definition: 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>)
alternative label: trans-heterozygous
in subset: agr_zyg

obsolete reagent sequence feature
type: Class
definition: 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)
editor note: replaced with SO:engineered_region
alternative label: extra-genomic sequence
deprecated: true

simple heterozygous
type: Class
subclass of: heterozygous
in subset: agr_zyg
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/+>)

transgene part
type: Class
equivalent class: Class
  intersection of: gene part
  intersection of: Restriction
    on property: is subsequence of
    some values from: transgene
subclass of: gene part
subclass of: Restriction
  on property: is subsequence of
  some values from: transgene
definition: A structurally or functionally defined component of a transgene (e.g. a promoter, a region coding for a fluorescent protein tag, etc)

variant
type: Class
subclass of: variation attribute
definition: An attribute inhering in a sequence feature that varies from some designated reference in virtue of alterations in its sequence or expression level

polymorphic
type: Class
subclass of: variation attribute
definition: 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.

mutant
type: Class
subclass of: variation attribute
definition: 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.

genomic feature
type: Class
equivalent class: Class
  intersection of: sequence_feature
  intersection of: Restriction
    on property: has_location
    some values from: genomic feature location
subclass of: genomic entity
subclass of: sequence_feature
subclass of: Restriction
  on property: is part of
  some values from: genome
subclass of: Restriction
  on property: has_sequence
  some values from: genomic sequence
subclass of: Restriction
  on property: has_location
  some values from: genomic feature location
definition: 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)
editor note: 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.
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. 2. 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). 3. 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.

genetic material
type: Class
subclass of: nucleic acid
has curation status: exploratory term
definition: 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.

obsolete mutant allele
type: Class
has curation status: exploratory term
definition: 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.
definition source: Based on use of 'mutant' as described in PMID: 25741868 ACMG Guidelines
has obsolescence reason: Not required for any specific use case at this point so removed for simplicity. Formely asserted as allele and inferred as varaint allele. Eq class definition: allele and (mutation or ('has subsequence' some mutation))
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.
deprecated: true

mutation
type: Class
subclass of: sequence_alteration
subclass of: Restriction
  on property: varies_with
  some values from: wild-type allele
definition: 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.

extrachromosomal replicon
type: Class
equivalent class: Class
  intersection of: genomic feature
  intersection of: Class
    complement of: Restriction
      on property: is_proper_part_of
      some values from: chromosome
  intersection of: Restriction
    on property: has_sequence_attribute
    some values from: heritable
subclass of: genomic feature
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: heritable
definition: 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)
editor note: Consider replacing with SO_0001038 ! extrachromosomal_mobile_genetic_element
alternative label: episomal replicon
has obsolescence reason: 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'.

expression construct
type: Class
subclass of: engineered genetic construct
alternative label: expression construct feature

polymorphic allele
type: Class
subclass of: allele
definition: 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.
definition source: PMID: 25741868 ACMG Guidelines
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%).

major polymorphic allele
type: Class
subclass of: polymorphic allele
definition: A polymorphic allele that is present at the highest frequency relative to other polymorphic variants at the same genomic location.
alternative label: major allele

minor polymorphic allele
type: Class
subclass of: polymorphic allele
definition: 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).
alternative label: minor allele

ancestral polymorphic allele
type: Class
subclass of: polymorphic allele
definition: A polymorphic allele that is determined from the sequence of a recent ancestor in a phylogentic tree.
alternative label: ancestral allele

wild-type allele
type: Class
subclass of: allele
definition: 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.
alternative label: wild-type allele
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. The 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.

wild-type gene
type: Class
subclass of: wild-type allele
subclass of: gene
alternative label: wild-type gene allele
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.

reagent targeted gene
type: Class
subclass of: expression-variant gene
subclass of: Restriction
  on property: has_proper_part
  some values from: reagent-targeted gene subregion
subclass of: Restriction
  on property: is_gene_target_of
  some values from: gene knockdown reagent
definition: 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.

transiently-expressed transgene
type: Class
subclass of: expression-variant gene
definition: 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).
alternative label: experimentally-expressed transgene
alternative label: extrinsic transgene

wild-type
type: Class
subclass of: variation attribute
definition: 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.

allele
type: Class
equivalent class: Class
  intersection of: genomic feature
  intersection of: Restriction
    on property: varies_with
    some values from: genomic feature
subclass of: genomic feature
subclass of: Restriction
  on property: varies_with
  some values from: genomic feature
definition: One of a set of sequence features known to exist at a particular genomic location.
editor note: 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. To 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. [1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) [2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) [3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) [4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) [5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) [6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) [6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 [7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) [8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) [9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) [10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) [11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)
alternative label: variable feature
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). Alleles 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).

aneusomic
type: Class
subclass of: variation attribute
has curation status: exploratory term
definition: 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.

variant gene allele
type: Class
equivalent class: Class
  intersection of: gene allele
  intersection of: Restriction
    on property: varies_with
    some values from: reference allele
subclass of: variant allele
subclass of: gene allele
subclass of: Restriction
  on property: has_variant_part
  some values from: sequence_alteration
subclass of: Restriction
  on property: is_variant_allele_of
  some values from: gene
definition: 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.

single locus complement
type: Class
subclass of: genomic feature set
example of usage: The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome.
definition: 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.
editor note: TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label.
alternative label: allelic complement
alternative label: homologous allele complement
alternative label: single locus feature complement
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. The 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.

extrinsic genotype
type: Class
subclass of: genotype
example of usage: 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: shha<MO1-1ng/ul>; shhb<pFLAG-mmusShhb> This 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.
definition: A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state.
editor note: 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. Our 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. Finally, 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."
alternative label: experimental genotype
alternative label: expression genotype
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. The '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.

effective genotype
type: Class
subclass of: genotype
subclass of: Restriction
  on property: has part
  some values from: extrinsic genotype
subclass of: Restriction
  on property: has part
  some values from: intrinsic genotype
definition: 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).
editor note: 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."
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.

reagent-targeted gene complement
type: Class
subclass of: qualified genomic feature set
subclass of: Restriction
  on property: has member
  some values from: reagent targeted gene
definition: 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.

transiently-expressed transgene complement
type: Class
subclass of: qualified genomic feature set
subclass of: Restriction
  on property: has_variant_part
  some values from: transiently-expressed transgene
definition: The set of all transgenes trransiently expressed in a biological system in the context of a given experiment.
alternative label: experimental transgene complement

expression-variant gene
type: Class
subclass of: expression-qualified sequence feature
subclass of: Restriction
  on property: is_expression_variant_of
  some values from: gene
example of usage: 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).
definition: 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).
editor note: 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.
alternative label: expression allele
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). The 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.

gene knockdown reagent
type: Class
subclass of: engineered_region
alternative label: gene targeting reagent
alternative label: sequence targeting reagent

reagent-targeted gene subregion
type: Class
subclass of: expression-qualified sequence feature
definition: A region within a gene that is specifically targeted by a gene knockdown reagent, typically in virtue of bearing sequence complementary to the reagent.
alternative label: targeted gene segment

genotype
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: Class
    union of: genomic feature set
    union of: qualified genomic feature set
definition: 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.
editor note: 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.
definition source: 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). Note however that the VMC genotype concept likely is not intended to cover 'effective' and 'extrinsic' genotype concepts defined in GENO.
comment: 1. Scope of 'Genetic State': '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. 2. Genotype Subtypes: In 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. Two 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. 3. The Genotype Partonomy: '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 compl…

zebrafish phenotype
type: Class
subclass of: 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 This 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.

homoplasmic
type: Class
subclass of: organellar plasmy
definition: an allelic state where a single allele exists at a particular location in the organellar genome (mitochondrial or plastid) of a cell/organism.
in subset: agr_zyg

heteroplasmic
type: Class
subclass of: organellar plasmy
definition: 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.
in subset: agr_zyg

hemizygous X-linked
type: Class
subclass of: hemizygous
in subset: agr_zyg

hemizygous Y-linked
type: Class
subclass of: hemizygous
in subset: agr_zyg

hemizygous insertion-linked
type: Class
subclass of: hemizygous
in subset: agr_zyg

genomic background
type: Class
equivalent class: Class
  intersection of: genomic genotype
  intersection of: Restriction
    on property: sequence role
    some values from: reference
subclass of: genomic genotype
subclass of: Restriction
  on property: sequence role
  some values from: reference
subclass of: Restriction
  on property: denotes
  some values from: background genome
definition: A genomic genotype that specifies the baseline sequence of a genome from which a variant genome is derived (through the introduction of sequence alterations).
editor note: 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.
alternative label: background genotype

chromosomal region
type: Class
subclass of: chromosome part
subclass of: Restriction
  on property: is part of
  some values from: chromosome arm
example of usage: 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".
definition: 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.
editor note: New term request for SO.
definition source: 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: chromosome > arm > region > band > sub-band Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): chromosome > arm > band > sub-band > sub-sub-band

chromosome sub-band
type: Class
subclass of: chromosome part
subclass of: Restriction
  on property: is part of
  some values from: chromosome band
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: chromosomal band intensity
example of usage: 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".
definition source: 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: chromosome > arm > region > band > sub-band Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): chromosome > arm > band > sub-band > sub-sub-band

chromosomal band intensity
type: Class
subclass of: sequence feature attribute
alternative label: chromosomal band brightness

gpos
type: Class
subclass of: chromosomal band intensity

gneg
type: Class
subclass of: chromosomal band intensity

gvar
type: Class
subclass of: chromosomal band intensity

gpos100
type: Class
subclass of: gpos

gpos75
type: Class
subclass of: gpos

gpos50
type: Class
subclass of: gpos

gpos25
type: Class
subclass of: gpos

short chromosome arm
type: Class
subclass of: chromosome arm
definition: A chromosome arm that is the shorter of the two arms of a given chromosome.
alternative label: p-arm
alternative label: stalk

long chromosome arm
type: Class
subclass of: chromosome arm
definition: A chromosome arm that is the longer of the two arms of a given chromosome.
alternative label: q-arm

gpos66
type: Class
subclass of: gpos

gpos33
type: Class
subclass of: gpos

regulatory transgene region
type: Class
subclass of: transgene part
subclass of: regulatory_region
definition: A transgene part whose sequence regulates the synthesis of a functional product, but which is not itself transcribed.

expressed transgene region
type: Class
subclass of: transgene part
definition: A transgene part whose sequence is expressed in a gene product through transcription and/or translation.
alternative label: coding transgene feature

reporter region
type: Class
subclass of: expressed transgene region

selectable marker transgene
type: Class
equivalent class: Class
  intersection of: transgene
  intersection of: Restriction
    on property: has_sequence_attribute
    some values from: selectable marker
subclass of: engineered_region
subclass of: transgene
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: selectable marker
definition: A transgene whose product is used as a selectable marker.

karyotype
type: Class
subclass of: genomic genotype
definition: 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.
definition source: Derived from http://en.wikipedia.org/wiki/Karyotype (accessed 2017-03-28)
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). A 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).

genomic genotype (sex-qualified)
type: Class
subclass of: genomic genotype
subclass of: Restriction
  on property: has_sex_agnostic_part
  some values from: genomic genotype (sex-agnostic)
definition: A genomic genotype where the genomic background specifies a male or female sex chromosome complement.
editor note: 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). 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. 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.
alternative label: intrinsic genotype (sex-specific)
alternative label: sex-qualified genotype
alternative label: sex-qualified intrinsic genotype
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. Conceptually, 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.

male intrinsic genotype
type: Class
subclass of: genomic genotype (sex-qualified)
definition: A genomic genotype here the genomic background specifies a male sex chromosome complement.

female intrinsic genotype
type: Class
subclass of: genomic genotype (sex-qualified)
definition: A genomic genotype here the genomic background specifies a female sex chromosome complement.

unspecified genomic background
type: Class
subclass of: genomic background
definition: A background genotype whose sequence or identity is not known or specified.
alternative label: unspecified background genotype

sequence feature set
type: Class
subclass of: sequence feature or set
subclass of: Restriction
  on property: has member
  some values from: sequence_feature
subclass of: Restriction
  on property: has_member_count
  some values from: int
example of usage: 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 2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. 3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}
definition: 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). The 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]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270

genomic feature set
type: Class
subclass of: sequence feature set
subclass of: genomic entity
subclass of: Restriction
  on property: has member
  some values from: genomic feature
definition: A set of genomic features (i.e. sequence features that are of genomic origin).
editor note: 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.
alternative label: genomic locus complement
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. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.

gene part
type: Class
equivalent class: Class
  intersection of: genomic feature
  intersection of: Restriction
    on property: is subsequence of
    some values from: gene allele
subclass of: genomic feature
subclass of: sequentially ordered entity
subclass of: Restriction
  on property: is subsequence of
  some values from: gene allele
definition: 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).
alternative label: defined gene part
database_cross_reference: SO:0000831 (gene member region)

reporter transgene
type: Class
equivalent class: Class
  intersection of: transgene
  intersection of: Restriction
    on property: has_sequence_attribute
    some values from: reporter
subclass of: engineered_region
subclass of: transgene
subclass of: Restriction
  on property: has part
  some values from: reporter region
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: reporter
definition: A transgene that codes for a product used as a reporter of gene expression or activity.

obsolete null feature
type: Class
example of usage: A junction between bases, a deletion variant, a terminus at the end of a chromosome.
definition: A genomic feature that has an extent of zero.
editor note: Former logical def: 'genomic feature' and (has_extent value 0)
deprecated: true

novel extrachromosomal replicon
type: Class
subclass of: extrachromosomal replicon
subclass of: novel replicon
subclass of: Class
  complement of: Restriction
    on property: is_proper_part_of
    some values from: chromosome
definition: 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.
alternative label: aberrant extrachromosomal replicon
alternative label: exogenous extrachromosomal replicon
alternative label: transgenic extrachromosomal replicon
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'.

novel replicon
type: Class
subclass of: sequence_alteration
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: novel
has curation status: exploratory term
definition: A genomic feature that represents an entirely new replicon in the genome, e.g. an extrachromosomal replicon or an extra copy of a chromosome.
editor note: 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.
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.

novel
type: Class
subclass of: variation attribute
definition: 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.

terminus
type: Class
subclass of: sequence_feature
definition: 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).

sequence feature or set
type: Class
equivalent class: Class
  union of: sequence feature or set
  union of: sequence_feature
subclass of: generically dependent continuant
definition: A sequence feature or a set of such features.
alternative label: sequence feature or collection
comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. '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). 3. '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.

biological sequence
type: Class
subclass of: biological sequence or set
subclass of: Restriction
disjoint with: sequence feature location
disjoint with: sequence_feature
definition: A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).
editor note: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. '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). 3. '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).
alternative label: biomacromolecular sequence
alternative label: state
database_cross_reference: VMC:State
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.

Axiom
annotated source: biological sequence
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true

Axiom
annotated source: biological sequence
annotated property: alternative label
annotated target: state
editor note: In the VMC model, the notion of a GENO:biological sequence is called the 'state' of an allele.

qualified sequence feature or collection
type: Class
subclass of: generically dependent continuant
definition: 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.

qualified genomic feature
type: Class
subclass of: genomic entity
subclass of: qualified sequence feature
subclass of: Restriction
example of usage: 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).
definition: A qualified sequence feature that carries sequence derived from the genome of a cell or organism.

Axiom
annotated source: qualified genomic feature
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true
comment: This axiom is an initial attempt to formalize the identity criteria of an extrinnsic context that separates qualified sequence features from sequence features (i.e. the context of its material bearer). As we further develop our efforts here this will get refined and more precise.

Axiom
annotated source: qualified genomic feature
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: 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).

qualified genomic feature set
type: Class
subclass of: genomic entity
subclass of: qualified sequence feature set
subclass of: Restriction
  on property: has_sequence_feature
  some values from: genomic feature set
subclass of: Restriction
  on property: has member
  some values from: qualified genomic feature
definition: A set of qualified sequence features that carry genomic sequence.
editor note: 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.
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. A 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.

intrinsic genotype
type: Class
subclass of: genotype
subclass of: Restriction
  on property: denotes
  some values from: Class
    union of: single locus complement
    union of: genome
editor note: 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.
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. 2. '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.

DNA sequence
type: Class
equivalent class: Class
  intersection of: biological sequence
  intersection of: Restriction
    on property: has_sequence_unit
    some values from: DNA residue
  intersection of: Restriction
    on property: has_sequence_unit
    all values from: DNA residue
subclass of: biological sequence
subclass of: Restriction
  on property: has_sequence_unit
  some values from: DNA residue

RNA sequence
type: Class
equivalent class: Class
  intersection of: biological sequence
  intersection of: Restriction
    on property: has_sequence_unit
    some values from: RNA residue
  intersection of: Restriction
    on property: has_sequence_unit
    all values from: RNA residue
subclass of: biological sequence
subclass of: Restriction
  on property: has_sequence_unit
  some values from: RNA residue

amino acid sequence
type: Class
equivalent class: Class
  intersection of: biological sequence
  intersection of: Restriction
    on property: has_sequence_unit
    some values from: amino acid residue
  intersection of: Restriction
    on property: has_sequence_unit
    all values from: amino acid residue
subclass of: biological sequence
subclass of: Restriction
  on property: has_sequence_unit
  some values from: amino acid residue

obsolete biological sequence or collection
type: Class
deprecated: true

obsolete biological sequence collection
type: Class
deprecated: true

location-qualified sequence feature
type: Class
subclass of: qualified genomic feature
has curation status: exploratory term
definition: 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).

expression-qualified sequence feature
type: Class
subclass of: qualified genomic feature
definition: 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)

obsolete genomic position
type: Class
definition: 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.
editor note: 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.
alternative label: genomic coordinates
has obsolescence reason: remodeling notion of sequence feature position around the idea of a 'genomic locus'
deprecated: true

phenotypic inheritance process
type: Class
subclass of: biological process
has curation status: exploratory term

obsolete unspecified
type: Class
definition: A sequence attribute inhering in a feature whose identity is not specified.
deprecated: true

variation attribute
type: Class
subclass of: sequence feature attribute
definition: An attribute describing a type of variation inhering in a sequence feature or collection.
alternative label: allele attribute

variant genomic genotype
type: Class
equivalent class: Class
  intersection of: genomic genotype
  intersection of: Restriction
    on property: denotes
    some values from: variant genome
subclass of: genomic genotype
subclass of: Restriction
  on property: denotes
  some values from: variant genome
definition: An intrinsic genotype that specifies variation from a defined reference genome.

obsolete sequence information entity
type: Class
definition: 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.
has obsolescence reason: eliminating classes that are not necessary or add uneeded complexity.
deprecated: true

biological sequence unit
type: Class
equivalent class: Class
  intersection of: biological sequence
  intersection of: Restriction
    on property: has_extent
    has value: 1
subclass of: biological sequence
alternative label: biological sequence residue
alternative label: monomeric residue

DNA residue
type: Class
subclass of: biological sequence unit
alternative label: deoxyribonucleic acid residue

RNA residue
type: Class
subclass of: biological sequence unit
alternative label: ribonucleic acid residue

amino acid residue
type: Class
subclass of: biological sequence unit

sequence feature attribute
type: Class
subclass of: specifically dependent continuant
definition: An attribute, quality, or state of a sequence feature or collection.
database_cross_reference: http://purl.obolibrary.org/obo/SO_0000400
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.

sequence feature location
type: Class
subclass of: generically dependent continuant
disjoint with: sequence_feature
definition: 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). 2. 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.

modification-qualified sequence feature
type: Class
subclass of: qualified genomic feature
has curation status: exploratory term
definition: 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)

allelic genotype
type: Class
equivalent class: Class
  intersection of: intrinsic genotype
  intersection of: Restriction
    on property: denotes
    some values from: single locus complement
subclass of: intrinsic genotype
subclass of: genomic entity
subclass of: Restriction
  on property: denotes
  some values from: single locus complement
example of usage: 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). 2. 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. ##fileformat=VCFv4.2 ##FORMAT=<ID=GT, Description="Genotype, 0=REF, 1=ALT"> #CHROM POS REF ALT FILTER FORMAT SAMP001 20 2300608 C T PASS GT 0/1 20 2301308 T G PASS GT 1/1 (derived from https://faculty.washington.edu/browning/beagle/intro-to-vcf.html) 3. 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.
definition: 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.
alternative label: single locus genotype
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. This 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.

genotype-phenotype association
type: Class
subclass of: association
subclass of: Restriction
has curation status: exploratory term
editor note: Exploratory class looking at creating more specific subtypes of associatiosn, and defining identity criteria for each.

Axiom
annotated source: genotype-phenotype association
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true

Axiom
annotated source: genotype-phenotype association
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true

Axiom
annotated source: genotype-phenotype association
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true

Axiom
annotated source: genotype-phenotype association
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true

knockdown reagent targeted gene complement
type: Class
subclass of: reagent-targeted gene complement
subclass of: Restriction
  on property: has_variant_part
  some values from: reagent targeted gene

obsolete coding sequence alteration
type: Class
has curation status: exploratory term
definition: A sequence alteration within the coding sequence of a gene.
has obsolescence reason: Not required at this poitn, so marked exploratory and obsoleted. Asserted under sequence_alteration.
deprecated: true

P-element construct
type: Class
subclass of: engineered genetic construct
definition: A construct that contains a mobile P-element, holding sequences to be delivered to a target cell or genome.

engineered genetic construct
type: Class
subclass of: engineered_region
definition: An engineered region that is used to transfer foreign genetic material into a host cell.
alternative label: engineered_genetic_vector
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. Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors.

extra-chromosomal transgene
type: Class
subclass of: transgene
definition: A transgene that is not chromosomally integrated in the host genome, but instead exists as part of an extra-chromosomal construct.
alternative label: non-integrated transgene

obsolete sequence feature collection
type: Class
definition: A collection of more than one sequence feature.
database_cross_reference: http://purl.obolibrary.org/obo/SO_0001260 ! sequence_collection
deprecated: true

haplotype
type: Class
subclass of: genomic feature set
subclass of: Restriction
  on property: has member
  some values from: allele
definition: A set of discrete, genetically-linked sequence alterations that reside on the same chromosomal strand and are typically co-inherited within a haplotype block.
editor note: 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. Instead, we can create an 'allele set' class as the haplotype parent?
source: Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype.
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. 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': 1. 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. 2. 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/). 3. 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. Each 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 incl…

genomic sequence set
type: Class
subclass of: biological sequence set
definition: A set of genomic sequences (a biological sequence that is of genomic origin).
alternative label: copy number complement
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.

microsatellite alteration
type: Class
subclass of: repeat region alteration

repeat region alteration
type: Class
subclass of: sequence_alteration

allelic state
type: Class
subclass of: sequence feature attribute
definition: 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

obsolete genetic dosage
type: Class
alternative label: allelic dosage
alternative label: an attribute inhering in a feature based on the total number or relative stoichiometry of functional copies present in a particular genome.
alternative label: gene dosage
has obsolescence reason: Remodeled this concept as a 'genetic dosage complement' - a sequence-level class, as opposed to a sequence feature attribute.
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. Duplications 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.
deprecated: true

allele origin
type: Class
subclass of: sequence feature attribute
definition: 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.
alternative label: genetic origin
alternative label: variant origin

maternal allele origin
type: Class
subclass of: germline allele origin
definition: Describes an allele that is inherited from a female parent in virtue of the allele being present in the mother's egg.
alternative label: maternally inherited

paternal allele origin
type: Class
subclass of: germline allele origin
definition: Describes an allele that is inherited from a male parent in virtue of the allele being present in the father's sperm.
alternative label: paternally inherited

de novo allele origin
type: Class
subclass of: allele origin
definition: 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*.
definition source: Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/de-novo-mutation and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
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. De 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.

unknown allele origin
type: Class
subclass of: allele origin
definition: Describes an allele whose origin is not known.

somatic allele origin
type: Class
subclass of: allele origin
definition: 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.
alternative label: acquired
definition source: Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/somatic-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
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. These 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.

obsolete gametic
type: Class
definition: a quality inhering in a feature in virtue of its presence only in the genome of gametes (germ cells).
alternative label: germ-line
has obsolescence reason: replaced by GENO:0000900 ! 'germline'
deprecated: true

diplotype
type: Class
equivalent class: Class
  intersection of: allelic genotype
  intersection of: Restriction
    on property: denotes
    some values from: Class
      intersection of: single locus complement
      intersection of: Restriction
        on property: has member
        qualified cardinality: 2
        on class: allele
subclass of: allelic genotype
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: single locus complement
    intersection of: Restriction
      on property: has member
      qualified cardinality: 2
      on class: allele
definition: 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') Alt: 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." From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/

allelic phase
type: Class
subclass of: sequence feature attribute
definition: 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.

oryzias latipes strain
type: Class
subclass of: strain or breed
subclass of: Restriction
  on property: has member
  some values from: Oryzias latipes
subclass of: Restriction
  on property: has member
  all values from: Oryzias latipes

germline allele origin
type: Class
subclass of: inherited allele origin
definition: Describes an allele that is inherited from a parent in virtue of the allele being present in the germline of one of the parents.
alternative label: hereditary
alternative label: parental origin
alternative label: parentally inherited
definition source: Derived from https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/germline-variant and https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
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.

undetermined inheritance
type: Class
subclass of: inheritance pattern
definition: An inheritance pattern that is not determined or not known.
alternative label: unknown inheritance

obsolete canonical allele
type: Class
example of usage: 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”.
definition: One of a set of sequence features or haplotypes that exist at a particular genetic locus. <see ClinGen Allele Model>
editor note: 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.
definition source: http://dataexchange.clinicalgenome.org/allele/resource/canonical_allele/
has obsolescence reason: No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs.
source: ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)
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. In 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)
deprecated: true

obsolete contextual allele
type: Class
definition: An informational artifact that describes a canonical allele by defining its sequence and position relative to a particular reference sequence.
editor note: 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.
definition source: http://dataexchange.clinicalgenome.org/allele/resource/contextual_allele/
has obsolescence reason: No longer needed by ClinGen for their interpretation models, and will likely be replaced in ClinGen and elsewhere by VMC/GA4GH modeling constructs. Former axiom: denotes some 'obsolete_canonical allele'
source: ClinGen Allele Model (http://dataexchange.clinicalgenome.org/allele/)
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.
deprecated: true

heteroplasmic mitochondrial inheritance
type: Class
subclass of: mitochondrial inheritance
definition: A mitochondrial inheritance pattern whereby manifestation of a trait is observed when some inherited mitochondria contian the causative allele and some do not.

homoplasmic mitochondrial inheritance
type: Class
subclass of: mitochondrial inheritance
definition: A mitochondrial inheritance pattern whereby manifestation of a trait occurs when only mitochondria containing the causative allele are inherited.

genomic entity
type: Class
equivalent class: Class
  union of: genomic feature
  union of: Restriction
    on property: has part
    some values from: genomic feature
  union of: Restriction
    on property: has_sequence_feature
    some values from: Class
      union of: genomic feature
      union of: genomic feature set
  union of: Restriction
    on property: denotes
    some values from: Class
      union of: genomic feature
      union of: genomic feature set
      union of: qualified genomic feature set
subclass of: generically dependent continuant
subclass of: Restriction
  on property: in taxon
  some values from: organism
mixin: true
definition: An generically dependent continuant that carries biological sequence that is part of or derived from a genome.
editor note: 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.

haplotype block
type: Class
subclass of: genomic feature
definition: 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.
editor note: Consider whether we might better model a 'haplotype block' at the level of a sequence location, rather than a sequence region - e.g. as "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. Current 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.
definition source: Informed by http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block, and DOI: 10.1126/science.1069424.
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.

genomic genotype
type: Class
equivalent class: Class
  intersection of: intrinsic genotype
  intersection of: Restriction
    on property: denotes
    some values from: genome
subclass of: intrinsic genotype
subclass of: genomic entity
subclass of: Restriction
  on property: has_reference_part
  some values from: genomic background
subclass of: Restriction
  on property: denotes
  some values from: genome
definition: 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.
editor note: 'Genomic Genotype' vs 'Genome' in GENO: A 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.
alternative label: complete 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. 2. '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.

obsolete allele cellular context
type: Class
definition: 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)
has obsolescence reason: decided this attribute is not needed, and moved its child 'germline' and 'somatic' concepts under allele origin
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.
deprecated: true

genomic feature location
type: Class
subclass of: sequence feature location
definition: The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
editor note: 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. We 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.
editor note: 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. For 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).
alternative label: genomic location
alternative label: genomic locus
database_cross_reference: VMC:Location
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. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.

organismal entity
type: Class
equivalent class: Class
  union of: organism
  union of: Restriction
    on property: derives from
    some values from: organism
  union of: Restriction
    on property: has member
    some values from: organism
subclass of: material entity
mixin: true
has curation status: exploratory term
definition: 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).
editor note: useful organizational term to collect entities that have genomes/genotypes.

gene product
type: Class
subclass of: sequence_feature
definition: The molecular product resulting from transcription of a single gene (either a protein or RNA molecule)

reporter
type: Class
subclass of: sequence feature attribute

selectable marker
type: Class
subclass of: sequence feature attribute

selectable marker region
type: Class
subclass of: expressed transgene region

reference genome
type: Class
subclass of: genome
subclass of: Restriction
  on property: has_sequence
  some values from: reference genome sequence
definition: A genome whose sequence is identical to that of a genome sequence considered to be the reference.

obsolete haplotype
type: Class
definition: 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.
editor note: 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."
definition source: Informed by https://isogg.org/wiki/Haplotype and https://en.wikipedia.org/wiki/Haplotype and http://purl.obolibrary.org/obo/SO_0001024 ! haplotype.
has obsolescence reason: Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets. Former SC axioms: - is_allele_of some 'haplotype block' - 'has part' some sequence_alteration
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). 2. 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. GENO'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. 3. 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': a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire…
deprecated: true

obsolete haplotype block
type: Class
definition: 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.
definition source: Derived from DOI: 10.1126/science.1069424 and http://purl.obolibrary.org/obo/SO_0000355 ! haplotype_block.
has obsolescence reason: Decided to represent haplotypes as collections of discrete alleles, rather than continuous features defined by such sets.
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'. 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. ----------------------- * 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.
deprecated: true

organellar plasmy
type: Class
subclass of: allelic state
definition: 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.
in subset: agr_zyg
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.

qualified sequence feature
type: Class
subclass of: qualified sequence feature or collection
example of usage: 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).
definition: 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. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. '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). 3. '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.

qualified sequence feature set
type: Class
subclass of: qualified sequence feature or collection
subclass of: Restriction
  on property: has part
  some values from: qualified sequence feature
subclass of: Restriction
  on property: has_sequence_feature
  some values from: sequence feature set
definition: 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'.

biological sequence or set
type: Class
subclass of: generically dependent continuant
definition: A biolocical sequence, or set of such sequences.
alternative label: biological sequence or collection

biological sequence set
type: Class
subclass of: biological sequence or set
definition: 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'. A 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.

obsolete functional copy number complement
type: Class
definition: A set of all features representing *functional* versions of a specified sequence (typically that of a gene) in a particular genome.
editor note: 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."
alternative label: functional feature complement
alternative label: genetic dosage
has obsolescence reason: Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000963.
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.
deprecated: true

obsolete intrinsic sequence feature attribute
type: Class
definition: 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.
deprecated: true

obsolete extrinsic sequence feature attribute
type: Class
definition: 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.)
deprecated: true

allelic cellular distribution
type: Class
subclass of: sequence feature attribute
definition: 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).

constitutional
type: Class
subclass of: allelic cellular distribution
definition: A cellular distribution in which an allele is found in all cells of an organism's body, typically in virtue of its germline origin.

clonal
type: Class
subclass of: allelic cellular distribution
definition: 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.

multifactorial inheritance
type: Class
subclass of: inheritance pattern
definition: 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.
alternative label: complex inherritance
alternative label: multi-factorial inheritance
alternative label: multi-genic inheritance
alternative label: multi-locus inheritance
alternative label: multigenic inheritance
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001426
comment: Diseases inherited in this manner are termed 'complex diseases'.

digenic inheritance
type: Class
subclass of: multifactorial inheritance
definition: A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in two genes.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0010984

oligogenic inheritance
type: Class
subclass of: multifactorial inheritance
definition: A multifactorial inheritance pattern that is determined by the simultaneous action of alleles in few genes.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0010983
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.

polygenic inheritance
type: Class
subclass of: multifactorial inheritance
definition: A multifactorial inheritance pattern that is determined by the simultaneous action of alleles a large number of genes.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0010982
comment: Typically used for traits/conditions governed by more than three gene loci.

monogenic inheritance
type: Class
subclass of: inheritance pattern
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene, possibly together with environmental factors.
alternative label: single-gene inheritance

autosomal inheritance
type: Class
subclass of: monogenic inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a non-sex chromosome.

allosomal inheritance
type: Class
subclass of: monogenic inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a sex chromosome.
alternative label: gonosomal inheritance
database_cross_reference: http://purl.obolibrary.org/obo/HP_0010985

X-linked inheritance
type: Class
subclass of: allosomal inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on an X-chromosome.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001417

complete X-linked dominant inheritance
type: Class
subclass of: X-linked dominant inheritance
definition: 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.

incomplete X-linked dominant inheritance
type: Class
subclass of: X-linked dominant inheritance
definition: 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.
alternative label: semi-dominant X-linked inheritance

co-dominant X-linked inheritance
type: Class
subclass of: X-linked dominant inheritance
definition: An X-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.

Y-linked inheritance
type: Class
subclass of: allosomal inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Y-chromosome.
alternative label: holandric inheritance
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001450

Z-linked inheritance
type: Class
subclass of: allosomal inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a Z-chromosome.

Z-linked dominant inheritance
type: Class
subclass of: Z-linked inheritance
definition: A Z-linked inheritance pattern wherein the trait manifests in heterozygotes.

complete Z-linked dominant inheritance
type: Class
subclass of: Z-linked dominant inheritance
definition: 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.

incomplete Z-linked dominant inheritance
type: Class
subclass of: Z-linked dominant inheritance
definition: 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.
alternative label: semi-dominant Z-linked inheritance

co-dominant Z-linked inheritance
type: Class
subclass of: Z-linked dominant inheritance
definition: An Z-linked dominant inheritance pattern wherein a heterozygous individual simultaneously expresses the distinct traits associated with each allele in the heterozygous locus.

Z-linked reccessive inheritance
type: Class
subclass of: Z-linked inheritance
definition: 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.

W-linked inheritance
type: Class
subclass of: allosomal inheritance
definition: An inheritance pattern wherein the trait is determined by alleles of a single causal gene on a W-chromosome.

mitochondrial inheritance
type: Class
subclass of: inheritance pattern
definition: An inheritance pattern observed for traits related to a gene encoded on the mitochondrial genome.
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001427
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).

sex-limited autosomal dominant inheritance
type: Class
subclass of: autosomal dominant inheritance
definition: 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).
database_cross_reference: http://purl.obolibrary.org/obo/HP_0001470

sex-limited autosomal recessive inheritance
type: Class
subclass of: autosomal recessive inheritance
definition: 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).
database_cross_reference: http://purl.obolibrary.org/obo/HP_0031362

allele set
type: Class
subclass of: genomic feature set
definition: 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'.

obsolete variant copy number complement
type: Class
definition: 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).
alternative label: copy number variation
has obsolescence reason: Decided to implement copy number related classes at the sequence level, rather than the sequence feature level.
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). Note 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.
deprecated: true

obsolete copy number complement
type: Class
definition: 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.
has obsolescence reason: Decided to implement copy number related classes at the sequence level, rather than the sequence feature level. Replaced by GENO:0000961.
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. 2. 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. 3. 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.
deprecated: true

genomic sequence
type: Class
equivalent class: Restriction
  on property: is_sequence_of
  some values from: genomic feature
subclass of: biological sequence
subclass of: Restriction
  on property: is_sequence_of
  some values from: genomic feature
definition: 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.

copy number complement
type: Class
subclass of: genomic sequence set
definition: 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.
editor note: 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. We 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).
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. 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 'copy number complements' representing the set of all copies of a particular sequence in a genome. The 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.

variant copy number complement
type: Class
subclass of: copy number complement
definition: A 'copy number complement' that has an abnormal number of members, as the result of deletion or duplication event(s).
editor note: 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). For 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.
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.

functional copy complement
type: Class
subclass of: genomic sequence set
definition: A set representing the complement of all functional versions of a specified sequence (typically that of a gene) in a particular genome.
alternative label: functional genetic dosage
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. '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. As 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.

mosaic
type: Class
subclass of: clonal
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.

sequence interval
type: Class
subclass of: information content entity
definition: A pair of integers representing start and end position of a location on a sequence coordinate system.

chromosomal inheritance
type: Class
subclass of: inheritance pattern
definition: An inheritance pattern wherein the trait is determined by inheritance of extra, missing, or re-arranged chromosomes possibly together with environmental factors.
definition source: The Alliance of Genomic Resources

chromosomal deletion inheritance
type: Class
subclass of: chromosomal inheritance
definition: 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.
definition source: Alliance of Genomic Resources

chromosomal duplication inheritance
type: Class
subclass of: chromosomal inheritance
definition: 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.
definition source: Alliance of Genomic Resources

chromosomal rearrangement inheritance
type: Class
subclass of: chromosomal inheritance
definition: 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.
definition source: Alliance of Genomic Resources

inherited allele origin
type: Class
subclass of: allele origin
has curation status: exploratory
definition: Describes an allele that is inherited from a parent.
editor note: Need to consider if/how this is different than 'germline allele origin'. One 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'

uniparental allele origin
type: Class
subclass of: inherited allele origin
has curation status: exploratory
definition: 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. https://en.wikipedia.org/wiki/Uniparental_inheritance

biparental allele origin
type: Class
subclass of: inherited allele origin
has curation status: exploratory
definition: 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.

nullizygous
type: Class
subclass of: disomic zygosity
definition: 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.
has_narrow_synonym: homozygous null
in subset: agr_zyg

molecular_function
type: Class
subclass of: process
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
editor note: This is the same as GO molecular function
label: gene product or complex activity

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
database_cross_reference: GOC:pdt

biological_process
type: Class
subclass of: process
disjoint with: planned process
editor preferred label: biological_process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl
database_cross_reference: Wikipedia:Biological_process
label: biological process

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: GOC:pdt

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

developmental process
type: Class
subclass of: biological process
definition: 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]

human phenotypic abnormality
type: Class
subclass of: Phenotype
comment: pulling in HP 'phenotypic abnormality' root here

human life cycle stage
type: Class
subclass of: biological process
editor note: Stub class to serve as root of hierarchy for imports of human developmental stages from the Human Developmental Stages Ontology.
definition source: A spatiotemporal region encompassing some part of the life cycle of an organism.

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative label: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: A directive information entity that describes an action the bearer will take.
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: metadata incomplete
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.

software
type: Class
subclass of: plan specification
editor preferred label: software
has curation status: metadata complete
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
subclass of: Restriction
  on property: concretizes
  some values from: information content entity
editor preferred label: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative label: data

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
has curation status: pending final vetting
definition: A generically dependent continuant that is about some thing.
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: 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). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

dot plot
type: Class
subclass of: graph
editor preferred label: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred label: graph
has curation status: pending final vetting
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
term editor: PERSON: Lawrence Hunter
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266

source code module
type: Class
subclass of: directive information entity
editor preferred label: source code module
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
has curation status: metadata incomplete
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

data format specification
type: Class
subclass of: directive information entity
editor preferred label: data format specification
has curation status: metadata incomplete
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

image
type: Class
subclass of: figure
editor preferred label: image
has curation status: ready for release
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

data about an ontology part
type: Class
subclass of: data item
editor preferred label: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg
alternative label: ontology metadata

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content entity
editor preferred label: material information bearer
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
example of usage: a brain
example of usage: a hard drive
has curation status: ready for release
definition: A material entity in which a concretization of an information content entity inheres.
term editor: GROUP: IAO

histogram
type: Class
subclass of: graph
editor preferred label: histogram
has curation status: ready for release
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred label: heatmap
has curation status: ready for release
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

dendrogram
type: Class
subclass of: graph
editor preferred label: dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
has curation status: ready for release
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred label: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: ready for release
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
alternative label: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
editor preferred label: obsolescence reason specification
has curation status: pending final vetting
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

figure
type: Class
subclass of: information content entity
editor preferred label: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter

diagram
type: Class
subclass of: figure
editor preferred label: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: metadata complete
definition: A figure that expresses one or more propositions
term editor: PERSON: Lawrence Hunter

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
editor preferred label: denotator type
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
term editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

ontology module
type: Class
subclass of: data about an ontology part
editor preferred label: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative label: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
type: Class
subclass of: ontology module
editor preferred label: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred label: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred label: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred label: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred label: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred label: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative label: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred label: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative label: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative label: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred label: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred label: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred label: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred label: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred label: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred label: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred label: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred label: EL++ ontology module

mammalian phenotype
type: Class
subclass of: Phenotype
comment: where to place this depends on if we take the organismal view or the quality centric view.

Mus musculus
type: Class
subclass of: Murinae
editor preferred label: Mus musculus
alternative label: house mouse
alternative label: mouse
imported from: ncbitaxon.owl

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
comment: Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.

Euteleostomi
type: Class
subclass of: Vertebrata <vertebrates>
editor preferred label: Euteleostomi
alternative label: bony vertebrates
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative label: eubacteria
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative label: eucaryotes
alternative label: eukaryotes
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative label: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative label: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Opisthokonta
editor preferred label: Metazoa
alternative label: metazoans
alternative label: multicellular animals
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Metazoa
editor preferred label: Bilateria
imported from: ncbitaxon.owl

Murinae
type: Class
subclass of: Rodentia
editor preferred label: Murinae
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative label: mammals
imported from: ncbitaxon.owl

Vertebrata <vertebrates>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <vertebrates>
alternative label: Vertebrata
alternative label: vertebrates
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Euteleostomi
editor preferred label: Danio rerio
alternative label: leopard danio
alternative label: zebra danio
alternative label: zebra fish
alternative label: zebrafish
imported from: ncbitaxon.owl

Oryzias latipes
type: Class
subclass of: organism

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative label: human
alternative label: human being
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Euarchontoglires
editor preferred label: Rodentia
alternative label: rodent
imported from: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process that realizes a plan which is the concretization of a plan specification.
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: 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.
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

regulator role
type: Class
subclass of: regulatory role
editor preferred label: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has curation status: metadata complete
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
term editor: Person:Jennifer Fostel
alternative label: regulator
definition source: OBI

regulatory role
type: Class
subclass of: role
editor preferred label: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: metadata complete
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
term editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: metadata complete
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
term editor: PERSON:Jennifer Fostel
alternative label: material provider role
alternative label: supplier

classified data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class prediction data transformation
editor preferred label: classified data set
has curation status: pending final vetting
definition: A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: data set with assigned class labels

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
term editor: PERSON:Matthew Brush
alternative label: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative label: material transformation
definition source: OBI branch derived

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: ready for release
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013

population
type: Class
subclass of: taxonomic group
editor preferred label: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
definition: 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
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
subclass of: Restriction
  on property: has role
  some values from: regulator role
editor preferred label: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: ready for release
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative label: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
editor preferred label: manufacturing
has curation status: ready for release
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred label: manufacturing objective
has curation status: ready for release
definition: is the objective to manufacture a material of a certain function (device)
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred label: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: metadata incomplete
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
term editor: GROUP: Role Branch
definition source: OBI

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
editor preferred label: clustered data set
example of usage: A clustered data set is the output of a K means clustering data transformation
has curation status: pending final vetting
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative label: data set with assigned discovered class labels
curator note: AR thinks could be a data item instead

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative label: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop

class prediction data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: classified data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class prediction objective
subclass of: data transformation
editor preferred label: class prediction data transformation
has curation status: ready for release
definition: A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
term editor: James Malone
alternative label: supervised classification data transformation
definition source: PERSON: James Malone

portioning objective
type: Class
subclass of: material separation objective
disjoint with: separation into different composition objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters

support vector machine
type: Class
subclass of: class prediction data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: class prediction objective
editor preferred label: support vector machine
has curation status: metadata incomplete
definition: A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
term editor: James Malone
term editor: Ryan Brinkman
alternative label: SVM
definition source: PERSON: Ryan Brinkman

decision tree induction objective
type: Class
subclass of: data transformation objective
editor preferred label: decision tree induction objective
has curation status: metadata incomplete
definition: A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
term editor: James Malone

decision tree building data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: decision tree induction objective
editor preferred label: decision tree building data transformation
has curation status: metadata complete
definition: A decision tree building data transformation is a data transformation that has objective decision tree induction.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern software
type: Class
subclass of: software
editor preferred label: GenePattern software
has curation status: metadata complete
definition: a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
term editor: James Malone
term editor: Person:Helen Parkinson
definition source: WEB: http://www.broadinstitute.org/cancer/software/genepattern/

peak matching
type: Class
subclass of: data transformation
editor preferred label: peak matching
has curation status: metadata incomplete
definition: Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
term editor: James Malone
term editor: Ryan Brinkman
definition source: PERSON: Ryan Brinkman

k-nearest neighbors
type: Class
subclass of: dataset creating
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-nearest neighbors
has curation status: pending final vetting
definition: A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
term editor: James Malone
alternative label: k-NN
definition source: PERSON: James Malone

CART
type: Class
subclass of: decision tree building data transformation
editor preferred label: CART
has curation status: ready for release
definition: A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
term editor: James Malone
alternative label: classification and regression trees
definition source: BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.

statistical model validation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
subclass of: partitioning data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: cross validation objective
editor preferred label: statistical model validation
example of usage: Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
has curation status: metadata complete
definition: A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
term editor: Helen Parkinson
definition source: http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters

manufacturer
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: manufacturer role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: manufacturer
has curation status: metadata incomplete
definition: A person or organization that has a manufacturer role

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred label: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: metadata incomplete
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
term editor: PERSON:Helen Parkinson

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
comment: A tissue sample that has been sliced and stained for a histology study.

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has curation status: metadata complete
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters

questionnaire
type: Class
subclass of: document
editor preferred label: questionnaire
has curation status: metadata complete
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
term editor: PERSON: Jessica Turner
definition source: Merriam-Webster

secondary cultured cell
type: Class
subclass of: cultured cell
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: cell culture splitting
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: cell culture splitting
subclass of: Restriction
  on property: derives from
  some values from: primary cultured cell
editor preferred label: secondary cultured cell
has curation status: metadata complete
definition: A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
term editor: Person: Matthew Brush
definition source: PERSON: Matthew Brush
comment: A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.

establishing cell line
type: Class
subclass of: establishing cell culture
subclass of: Restriction
  on property: has_specified_output
  some values from: cell line
editor preferred label: establishing cell line
has curation status: metadata complete
definition: a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
editor note: 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
term editor: Person: Matthew Brush
definition source: PERSON:Matthew Brush

reagent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: reagent role
subclass of: processed material
subclass of: Restriction
  on property: has role
  some values from: reagent role
editor preferred label: reagent
has curation status: metadata complete
definition: A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
editor note: 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
comment: (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some…

secondary cultured cell population
type: Class
subclass of: cultured cell population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: cell culture splitting
subclass of: Restriction
  on property: has grain
  some values from: secondary cultured cell
subclass of: Restriction
  on property: has grain
  all values from: secondary cultured cell
editor preferred label: secondary cultured cell population
has curation status: metadata complete
definition: A cultured cell population that is derived through one or more passages in culture.
editor note: The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
term editor: PERSON:Matthew Brush
alternative label: secondary cell culture sample
definition source: PERSON:Matthew Brush
comment: The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: metadata complete
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters

collection of specimens
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has member
    all values from: specimen
subclass of: material entity
editor preferred label: collection of specimens
example of usage: Blood cells collected from multiple donors over the course of a study.
has curation status: pending final vetting
definition: A material entity that has two or more specimens as its parts.
editor note: Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: OBIB, OBI
source: Biobank

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to AJCC 7th edition
example of usage: G1:Well differentiated
example of usage: G4: Undifferentiated
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to the Fuhrman Nuclear Grading System
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade for ovarian tumor
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to a two-tier grading system
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to the World Health Organization
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for colon according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
term editor: Chris Stoeckert, Helena Ellis
alternative label: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: clinical tumor stage group according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Clinical FIGO stage
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

performance status value specification
type: Class
subclass of: categorical value specification
editor preferred label: performance status value specification
has curation status: metadata complete
definition: A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Performance Status Scale
definition source: https://en.wikipedia.org/wiki/Performance_status
ontology term requester: NCI BBRB

Eastern Cooperative Oncology Group score value specification
type: Class
subclass of: performance status value specification
editor preferred label: Eastern Cooperative Oncology Group score value specification
has curation status: metadata complete
definition: A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
term editor: Chris Stoeckert, Helena Ellis
alternative label: ECOG score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Karnofsky score vaue specification
type: Class
subclass of: performance status value specification
editor preferred label: Karnofsky score vaue specification
has curation status: metadata complete
definition: A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Karnofsky Score
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

material supplier
type: Class
equivalent class: Class
  intersection of: Class
    union of: Homo sapiens
    union of: organization
  intersection of: Restriction
    on property: has role
    some values from: material supplier role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: material supplier role
editor preferred label: material supplier
has curation status: metadata incomplete
definition: A person or organization that provides material supplies to other people or organizations.
term editor: Rebecca Jackson
term tracker item: https://github.com/obi-ontology/obi/issues/1289

Epstein Barr virus transformed B cell
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: establishing cell culture
      intersection of: Restriction
        on property: has_specified_input
        some values from: Viruses
  intersection of: Restriction
    on property: derives from
    all values from: B cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: establishing cell culture
    intersection of: Restriction
      on property: has_specified_input
      some values from: Viruses
editor preferred label: Epstein Barr virus transformed B cell
example of usage: PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
has curation status: metadata complete
definition: A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI Biomaterial Branch

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: organismal entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
editor note: Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: specimen role
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
term editor: PERSON:Matthew Brush
alternative label: cell culture sample
definition source: PERSON:Matthew Brush
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: ready for release
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative label: data analysis
alternative label: data processing
definition source: Branch editors
imported from: obi.owl

leave one out cross validation method
type: Class
subclass of: statistical model validation
editor preferred label: leave one out cross validation method
example of usage: The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
has curation status: metadata incomplete
definition: is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
term editor: Person:Helen Parkinson

k-means clustering
type: Class
subclass of: dataset creating
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: k-means clustering
has curation status: pending final vetting
definition: A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/K-means

hierarchical clustering
type: Class
subclass of: dataset creating
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: hierarchical clustering
has curation status: pending final vetting
definition: A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
term editor: James Malone
definition source: WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering

dimensionality reduction
type: Class
subclass of: dataset creating
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: dimensionality reduction
has curation status: ready for release
definition: A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative label: data projection
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

principal components analysis dimensionality reduction
type: Class
subclass of: dimensionality reduction
editor preferred label: principal components analysis dimensionality reduction
has curation status: ready for release
definition: A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative label: pca data reduction
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot

data visualization
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: graph
    union of: image
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    union of: graph
    union of: image
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
has curation status: ready for release
definition: An planned process that creates images, diagrams or animations from the input data.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Tina Boussard
alternative label: data encoding as image
alternative label: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
curator note: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone

partitioning data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
editor preferred label: partitioning data transformation
has curation status: metadata incomplete
definition: A partitioning data transformation is a data transformation that has objective partitioning.
term editor: James Malone
definition source: PERSON: James Malone

partitioning objective
type: Class
subclass of: data transformation objective
editor preferred label: partitioning objective
example of usage: A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
has curation status: ready for release
definition: A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi

class discovery data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: data transformation
editor preferred label: class discovery data transformation
has curation status: ready for release
definition: A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
term editor: James Malone
alternative label: clustering data transformation
alternative label: unsupervised classification data transformation
definition source: PERSON: James Malone

class discovery objective
type: Class
subclass of: data transformation objective
editor preferred label: class discovery objective
has curation status: ready for release
definition: A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
term editor: James Malone
alternative label: clustering objective
alternative label: discriminant analysis objective
alternative label: unsupervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

class prediction objective
type: Class
subclass of: data transformation objective
editor preferred label: class prediction objective
has curation status: ready for release
definition: A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
term editor: James Malone
alternative label: classification objective
alternative label: supervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone

cross validation objective
type: Class
subclass of: partitioning objective
editor preferred label: cross validation objective
has curation status: pending final vetting
definition: A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
term editor: James Malone
alternative label: rotation estimation objective
definition source: WEB: http://en.wikipedia.org/wiki/Cross_validation

clustered data visualization
type: Class
subclass of: data visualization
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: dot plot
    union of: histogram
    union of: heatmap
    union of: dendrogram
    union of: scatter plot
subclass of: Restriction
  on property: has_specified_input
  all values from: clustered data set
editor preferred label: clustered data visualization
has curation status: metadata incomplete
definition: A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
term editor: James Malone

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
term editor: Bjoern Peters
definition source: IEDB

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
editor preferred label: 'establishing cell culture'
has curation status: metadata complete
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

cell culture splitting
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: portioning objective
editor preferred label: cell culture splitting
example of usage: The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
has curation status: pending final vetting
definition: The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
term editor: PlanAndPlannedProcess Branch
alternative label: cell culture passaging
definition source: OBI branch derived
comment: An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

quality
type: Class
subclass of: specifically dependent continuant
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

obsolete color brightness
type: Class
editor note: 'Value' label chosen here according to http://www.uwgb.edu/heuerc/2D/ColorTerms.html
editor note: Was parent of chromosomal band intensity before moving this class to live as a sequence feature attribute.
alternative label: color value
deprecated: true

biological sex
type: Class
subclass of: organismal quality
editor preferred label: biological sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
imported from: pato.owl

female
type: Class
subclass of: phenotypic sex
editor preferred label: female
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: pato.owl

male
type: Class
subclass of: phenotypic sex
editor preferred label: male
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
editor preferred label: physical object quality
definition: A quality which inheres in a continuant.
imported from: pato.owl

phenotypic sex
type: Class
subclass of: biological sex
editor preferred label: phenotypic sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
imported from: pato.owl

organismal quality
type: Class
subclass of: physical object quality
editor preferred label: organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl

collection of organisms
type: Class
subclass of: organismal entity
subclass of: Restriction
  on property: has member
  some values from: organism
definition: 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).

family
type: Class
subclass of: collection of organisms
definition: A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.

sequentially ordered entity
type: Class
subclass of: Restriction
  on property: has subsequence
  some values from: sequence atomic unit
definition: Any entity that is ordered in discrete units along a linear axis.
term editor: https://orcid.org/0000-0002-6601-2165

sequence atomic unit
type: Class
subclass of: sequentially ordered entity
definition: Any individual unit of a collection of like units arranged in a linear order
term editor: https://orcid.org/0000-0002-6601-2165

system
type: Class
subclass of: material entity
definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.jbiomedsem.com/content/4/1/43

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative label: primary structure of sequence macromolecule
alternative label: sequence
imported from: so.owl

morpholino_oligo
type: Class
subclass of: gene knockdown reagent
definition: 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.

chromosome arm
type: Class
subclass of: chromosome part
subclass of: Restriction
  on property: is part of
  some values from: chromosome part
example of usage: 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".
definition: 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.
editor note: Formerly http://purl.obolibrary.org/obo/GENO_0000613, replaced by SO term.
definition source: 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: chromosome > arm > region > band > sub-band Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): chromosome > arm > band > sub-band > sub-sub-band

sequence_feature
type: Class
subclass of: sequence feature or set
subclass of: Restriction
definition: Any extent of continuous biological sequence.
editor note: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. '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). 3. '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).
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.

Axiom
annotated source: sequence_feature
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: true
comment: Formalizes the first identity criteria for a sequence feature of its sequence.

Axiom
annotated source: sequence_feature
annotated property: subClassOf
annotated target: Restriction
is_identity_criteria: 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).

obsolete assembly_component
type: Class
definition: A region of known length which may be used to manufacture a longer region.
deprecated: true

contig
type: Class
subclass of: sequence_assembly
editor preferred label: contig
definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
imported from: so.owl
label: obsolete contig
deprecated: true

deletion
type: Class
subclass of: sequence_alteration
subclass of: Restriction
  on property: has_extent
  has value: 0
definition: The point at which one or more contiguous nucleotides were excised.
alternative label: deleted_sequence
alternative label: nucleotide deletion
alternative label: nucleotide_deletion
imported from: so.owl
IAO alt id: SO:1000033
IAO id: SO:0000159
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Nucleotide_deletion

enhancer
type: Class
subclass of: regulatory_region

promoter
type: Class
subclass of: regulatory_region
definition: A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.

translocation
type: Class
subclass of: sequence_alteration
definition: A region of nucleotide sequence that has translocated to a new position.
alternative label: transchr
alternative label: translocated sequence
imported from: so.owl
IAO id: SO:0000199
IAO subset: DBVAR

simple_sequence_length_variation
type: Class
subclass of: sequence_length_variation
alternative label: SSLP
alternative label: simple sequence length polymorphism
alternative label: simple sequence length variation
imported from: so.owl
IAO id: SO:0000207

sequence_length_variation
type: Class
subclass of: substitution
alternative label: sequence length variation
imported from: so.owl
IAO id: SO:0000248

engineered_foreign_gene
type: Class
subclass of: gene
subclass of: engineered_region
editor note: See here for a list of engineered foreign genes in ZFIN: https://zfin.org/search?q=&fq=type_1%3A%22Engineered+Foreign+Gene%22&category=Any, See here for a list of engineered regions in ZFIN: https://zfin.org/search?q=&fq=type%3A%22Engineered+Region%22&category=Any Includes things like loxP sites, inducible promoters, ires elements, etc.

microsatellite
type: Class
subclass of: genomic feature
definition: A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
definition source: http://en.wikipedia.org/wiki/Microsatellite_%28genetics%29
comment: A defined feature that includes any type of VNTR or SSLP locus.

RNAi_reagent
type: Class
subclass of: gene knockdown reagent

chromosome
type: Class
subclass of: genomic feature
definition: 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.

chromosome band
type: Class
subclass of: chromosome part
subclass of: Restriction
  on property: is part of
  some values from: chromosomal region
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: chromosomal band intensity
example of usage: 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".
definition: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
definition source: 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: chromosome > arm > region > band > sub-band Note that an alternate nomenclature for this hierarchy is here (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html): chromosome > arm > band > sub-band > sub-sub-band
comment: "Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.

sequence_assembly
type: Class
subclass of: assembly
editor preferred label: sequence_assembly
definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
imported from: so.owl

centromere
type: Class
subclass of: chromosome part

obsolete engineered_plasmid
type: Class
editor note: 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.
deprecated: true

insertion
type: Class
subclass of: sequence_alteration
definition: The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
alternative label: insertion
alternative label: nucleotide insertion
alternative label: nucleotide_insertion
imported from: so.owl
IAO alt id: SO:1000034
IAO id: SO:0000667
IAO subset: DBVAR
IAO subset: SOFA

SNP
type: Class
subclass of: SNV
definition: 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.
alternative label: single nucleotide polymorphism
imported from: so.owl
IAO id: SO:0000694
IAO subset: SOFA

junction
type: Class
subclass of: sequence_feature
comment: A junction is a boundary between regions. A boundary has an extent of zero.

gene
type: Class
subclass of: genomic feature
definition: 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.
editor note: 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).
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.

QTL
type: Class
subclass of: genomic feature
definition: 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.
alternative label: quantitative trait locus

engineered
type: Class
subclass of: sequence feature attribute
definition: An attribute to describe a region that was modified in vitro.

engineered_region
type: Class
equivalent class: Class
  intersection of: sequence_feature
  intersection of: Restriction
    on property: has_sequence_attribute
    some values from: engineered
subclass of: sequence_feature
subclass of: Restriction
  on property: has_sequence_attribute
  some values from: engineered
alternative label: construct

chromosome part
type: Class
equivalent class: Class
  intersection of: genomic feature
  intersection of: Restriction
    on property: is_proper_part_of
    some values from: chromosome
subclass of: genomic feature
subclass of: Restriction
  on property: is_proper_part_of
  some values from: chromosome
definition: 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'.
alternative label: chromosomal feature
alternative label: gross chromosomal part

transgene
type: Class
subclass of: gene
definition: 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' Transgenic 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. In 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. For 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 conta…
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). Note 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.

MNP
type: Class
subclass of: substitution
definition: A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
alternative label: multiple nucleotide polymorphism
imported from: so.owl
IAO id: SO:0001013

copy_number_variation
type: Class
subclass of: sequence_alteration
definition: A variation that increases or decreases the copy number of a given region.
alternative label: CNP
alternative label: CNV
alternative label: copy number polymorphism
alternative label: copy number variation
imported from: so.owl
IAO id: SO:0001019
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Copy_number_variation

genome
type: Class
subclass of: genomic feature set
definition: 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)
editor note: 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.
alternative label: 'genome sequence'
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'.

sequence_alteration
type: Class
equivalent class: Class
  intersection of: allele
  intersection of: Restriction
    on property: completely_varies_with
    some values from: genomic feature
subclass of: allele
subclass of: Restriction
  on property: completely_varies_with
  some values from: genomic feature
example of usage: A few examples highlighting the distinction of 'sequence alterations' from their parent 'variant allele': 1. 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. 2. 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. 3. 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.
definition: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
alternative label: sequence variation
imported from: so.owl
IAO alt id: SO:1000004
IAO alt id: SO:1000007
IAO id: SO:0001059
IAO subset: SOFA
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. Alleles 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. 2. 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'. For 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. 3. 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.

transgenic_insertion
type: Class
subclass of: insertion
subclass of: Restriction
  on property: has part
  some values from: integrated transgene
definition: An insertion that derives from another organism, via the use of recombinant DNA technology.
alternative label: transgenic insertion
imported from: so.owl
IAO id: SO:0001218

assembly
type: Class
subclass of: experimental_feature
editor preferred label: assembly
definition: A region of the genome of known length that is composed by ordering and aligning two or more different regions.
imported from: so.owl

experimental_feature
type: Class
subclass of: region
editor preferred label: experimental_feature
definition: A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
has obsolescence reason: not currently needed to support modeling use cases. can re-introduce if becomes necessary.
imported from: so.owl
label: obsolete experimental_feature
deprecated: true

gene_trap_construct
type: Class
subclass of: engineered genetic construct
definition: 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.

promoter_trap_construct
type: Class
subclass of: engineered genetic construct
definition: 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.

enhancer_trap_construct
type: Class
subclass of: engineered genetic construct
definition: 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.

SNV
type: Class
subclass of: substitution
definition: SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist.
alternative label: single nucleotide variant
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Thu Oct 08 11:37:49 PDT 2009
IAO id: SO:0001483
IAO subset: SOFA

heritable_phenotypic_marker
type: Class
subclass of: genomic feature
definition: 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.

reference genome sequence
type: Class
subclass of: reference sequence
example of usage: 'GRCh37.p10' (a human reference genome build)
definition: A genome sequence that is used as a standard against which other genome sequences are compared, or into which alterations are intentionally introduced.

copy_number_gain
type: Class
subclass of: copy_number_variation
definition: A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.
alternative label: copy number gain
alternative label: gain
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Mon Feb 28 01:54:09 PST 2011
IAO id: SO:0001742
IAO subset: DBVAR

copy_number_loss
type: Class
subclass of: copy_number_variation
definition: A sequence alteration whereby the copy number of a given region is less than the reference sequence.
alternative label: copy number loss
alternative label: loss
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Mon Feb 28 01:55:02 PST 2011
IAO id: SO:0001743
IAO subset: DBVAR

UPD
type: Class
subclass of: sequence_alteration
definition: 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.
alternative label: UPD
alternative label: uniparental disomy
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Mon Feb 28 02:01:05 PST 2011
IAO id: SO:0001744
IAO subset: DBVAR
IAO xref: http:http\://en.wikipedia.org/wiki/Uniparental_disomy

maternal_uniparental_disomy
type: Class
subclass of: UPD
definition: 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.
alternative label: maternal uniparental disomy
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Mon Feb 28 02:03:01 PST 2011
IAO id: SO:0001745

paternal_uniparental_disomy
type: Class
subclass of: UPD
definition: 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.
alternative label: paternal uniparental disomy
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Mon Feb 28 02:03:30 PST 2011
IAO id: SO:0001746

complex_structural_alteration
type: Class
subclass of: structural_alteration
definition: A structural sequence alteration where there are multiple equally plausible explanations for the change.
alternative label: complex
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Wed Mar 23 03:21:19 PDT 2011
IAO id: SO:0001784
IAO subset: DBVAR

structural_alteration
type: Class
subclass of: sequence_alteration
imported from: so.owl
IAO created by: kareneilbeck
IAO creation date: Fri Mar 25 02:27:41 PDT 2011
IAO id: SO:0001785
IAO subset: DBVAR

regulatory_region
type: Class
subclass of: gene part
subclass of: region
editor preferred label: regulatory_region
definition: A region of sequence that is involved in the control of a biological process.
editor note: Formerly http://purl.obolibrary.org/obo/GENO_0000067, replaced with SO term.
alternative label: regulatory element
alternative label: regulatory gene region
imported from: so.owl

substitution
type: Class
subclass of: sequence_alteration
definition: Any change in genomic DNA caused by a single event.
imported from: so.owl
IAO id: SO:1000002
IAO subset: SOFA

complex_substitution
type: Class
subclass of: substitution
definition: 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.
alternative label: complex substitution
imported from: so.owl
IAO id: SO:1000005
IAO subset: SOFA

point_mutation
type: Class
subclass of: SNV
definition: A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
alternative label: point mutation
imported from: so.owl
IAO id: SO:1000008
IAO subset: SOFA
IAO xref: http://en.wikipedia.org/wiki/Point_mutation

transition
type: Class
subclass of: SNV
definition: 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.
imported from: so.owl
IAO id: SO:1000009

pyrimidine_transition
type: Class
subclass of: transition
definition: A substitution of a pyrimidine, C or T, for another pyrimidine.
alternative label: pyrimidine transition
imported from: so.owl
IAO id: SO:1000010

C_to_T_transition
type: Class
subclass of: pyrimidine_transition
definition: A transition of a cytidine to a thymine.
alternative label: C to T transition
imported from: so.owl
IAO id: SO:1000011

C_to_T_transition_at_pCpG_site
type: Class
subclass of: C_to_T_transition
definition: The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
alternative label: C to T transition at pCpG site
imported from: so.owl
IAO id: SO:1000012

T_to_C_transition
type: Class
subclass of: pyrimidine_transition
alternative label: T to C transition
imported from: so.owl
IAO id: SO:1000013

purine_transition
type: Class
subclass of: transition
definition: A substitution of a purine, A or G, for another purine.
alternative label: purine transition
imported from: so.owl
IAO id: SO:1000014

A_to_G_transition
type: Class
subclass of: purine_transition
definition: A transition of an adenine to a guanine.
alternative label: A to G transition
imported from: so.owl
IAO id: SO:1000015

G_to_A_transition
type: Class
subclass of: purine_transition
definition: A transition of a guanine to an adenine.
alternative label: G to A transition
imported from: so.owl
IAO id: SO:1000016

transversion
type: Class
subclass of: SNV
definition: Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
imported from: so.owl
IAO id: SO:1000017
IAO xref: http://en.wikipedia.org/wiki/Transversion

pyrimidine_to_purine_transversion
type: Class
subclass of: transversion
definition: Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
alternative label: pyrimidine to purine transversion
imported from: so.owl
IAO id: SO:1000018

C_to_A_transversion
type: Class
subclass of: pyrimidine_to_purine_transversion
definition: A transversion from cytidine to adenine.
alternative label: C to A transversion
imported from: so.owl
IAO id: SO:1000019

C_to_G_transversion
type: Class
subclass of: pyrimidine_to_purine_transversion
alternative label: C to G transversion
imported from: so.owl
IAO id: SO:1000020

T_to_A_transversion
type: Class
subclass of: pyrimidine_to_purine_transversion
definition: A transversion from T to A.
alternative label: T to A transversion
imported from: so.owl
IAO id: SO:1000021

T_to_G_transversion
type: Class
subclass of: pyrimidine_to_purine_transversion
definition: A transversion from T to G.
alternative label: T to G transversion
imported from: so.owl
IAO id: SO:1000022

purine_to_pyrimidine_transversion
type: Class
subclass of: transversion
definition: Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
alternative label: purine to pyrimidine transversion
imported from: so.owl
IAO id: SO:1000023

A_to_C_transversion
type: Class
subclass of: purine_to_pyrimidine_transversion
definition: A transversion from adenine to cytidine.
alternative label: A to C transversion
imported from: so.owl
IAO id: SO:1000024

A_to_T_transversion
type: Class
subclass of: purine_to_pyrimidine_transversion
definition: A transversion from adenine to thymine.
alternative label: A to T transversion
imported from: so.owl
IAO id: SO:1000025

G_to_C_transversion
type: Class
subclass of: purine_to_pyrimidine_transversion
definition: A transversion from guanine to cytidine.
alternative label: G to C transversion
imported from: so.owl
IAO id: SO:1000026

G_to_T_transversion
type: Class
subclass of: purine_to_pyrimidine_transversion
definition: A transversion from guanine to thymine.
alternative label: G to T transversion
imported from: so.owl
IAO id: SO:1000027

indel
type: Class
subclass of: sequence_alteration
definition: A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.
imported from: so.owl
IAO id: SO:1000032
IAO xref: http://en.wikipedia.org/wiki/Indel
comment: Indels can have a different number of bases than the corresponding reference sequence.

duplication
type: Class
subclass of: insertion
definition: 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.
alternative label: nucleotide duplication
alternative label: nucleotide_duplication
imported from: so.owl
IAO id: SO:1000035

inversion
type: Class
subclass of: sequence_alteration
definition: A continuous nucleotide sequence is inverted in the same position.
alternative label: inversion
imported from: so.owl
IAO id: SO:1000036
IAO subset: DBVAR
IAO subset: SOFA

direct_tandem_duplication
type: Class
subclass of: tandem_duplication
definition: A tandem duplication where the individual regions are in the same orientation.
alternative label: direct tandem duplication
imported from: so.owl
IAO id: SO:1000039

inverted_tandem_duplication
type: Class
subclass of: tandem_duplication
definition: A tandem duplication where the individual regions are not in the same orientation.
alternative label: inverted tandem duplication
alternative label: mirror duplication
imported from: so.owl
IAO id: SO:1000040

tandem_duplication
type: Class
subclass of: duplication
definition: A duplication consisting of 2 identical adjacent regions.
alternative label: erverted
alternative label: tandem duplication
imported from: so.owl
IAO id: SO:1000173
IAO subset: DBVAR

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: SCTID:362889002
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
database_cross_reference: http://dbpedia.org/ontology/AnatomicalStructure

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CARO:0000003

life cycle stage
type: Class
subclass of: biological process
subclass of: biological_process
editor preferred label: life cycle stage
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
editor note: Stub class to serve as root of hierarchy for imports of developmental stages from Uberon or taxon specific vocabularies such as ZFIN stages terms)
imported from: uberon.owl

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

anatomical entity
type: Class
equivalent class: Restriction
  on property: is anatomical entity
  has self: true
subclass of: organismal entity
subclass of: Restriction
  on property: derives from
  some values from: organism
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
editor note: Stub class to serve as root of hierarchy for imports of anatomical entities from UBERON, CARO, or taxon-specific anatomy ontologies.
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
database_cross_reference: http://purl.obolibrary.org/obo/CARO_0000000

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
database_cross_reference: FMA:62955
database_cross_reference: http://orcid.org/0000-0001-9114-8737

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

temperature unit
type: Class
subclass of: measurement unit label
editor preferred label: temperature unit
imported from: uo.owl

substance unit
type: Class
subclass of: measurement unit label
editor preferred label: substance unit
imported from: uo.owl

concentration unit
type: Class
subclass of: measurement unit label
editor preferred label: concentration unit
imported from: uo.owl

volume unit
type: Class
subclass of: measurement unit label
editor preferred label: volume unit
imported from: uo.owl

frequency unit
type: Class
subclass of: measurement unit label
editor preferred label: frequency unit
imported from: uo.owl

volumetric flow rate unit
type: Class
subclass of: measurement unit label
editor preferred label: volumetric flow rate unit
imported from: uo.owl

rate unit
type: Class
subclass of: measurement unit label
editor preferred label: rate unit
imported from: uo.owl

Phenotype
type: Class
subclass of: quality
editor note: Stub node that gathers root classes from various taxon-specific phenotype ontologies, as connectors to bringing classes from these ontolgies into the GENO framework.
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) 2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment
label: phenotype

worm phenotype
type: Class
subclass of: Phenotype
definition: Animals exhibit variations compared to a given control.
editor note: '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.
alternative label: Variant
alternative label: c. elegans phenotype

abnormal(ly) malformed endocardium cell
type: Class
subclass of: zebrafish phenotype

abnormal(ly) absent dorso-rostral cluster
type: Class
subclass of: zebrafish phenotype

abnormal(ly) disrupted diencephalon development
type: Class
subclass of: zebrafish phenotype

abnormal(ly) disrupted neutrophil aggregation
type: Class
subclass of: zebrafish phenotype

abnormal(ly) absent adaxial cell
type: Class
subclass of: zebrafish phenotype

association
type: Class
subclass of: information content entity

mus musculus shh gene
type: Class
subclass of: mus musculus gene
has curation status: exemplar term
comment: Equivalent to: http://www.informatics.jax.org/marker/MGI:98297

danio rerio shha gene
type: Class
subclass of: danio rerio gene
has curation status: exemplar term
database_cross_reference: http://zfin.org/ZDB-GENE-980526-166

danio rerio cdkn1ca gene
type: Class
subclass of: danio rerio gene
has curation status: exemplar term
database_cross_reference: http://zfin.org/ZDB-GENE-040123-1

homo sapiens SHH gene
type: Class
subclass of: homo sapiens gene
has curation status: exemplar term
comment: Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 Codes for: http://www.uniprot.org/uniprot/Q15465

Western Australian Mulga Shrublands Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1310
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1310

Australasia Ecoregion
type: NamedIndividual
database_cross_reference: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Tirari-Sturt Stony Desert Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1309
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1309

Simpson Desert Region
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1308
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1308

Pilbara Shrublands Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1307
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1307

Carnarvon Xeric Shrublands Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1301
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1301

Central Ranges Xeric Shrub Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1302
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1302

Gibson Desert Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1303
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1303

The Great Sandy-Tanami Desert Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1304
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1304

Great Victoria Desert Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1305
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1305

Nullarbor Plains Xeric Shrubland Ecoregion
type: NamedIndividual
is part of: Australasia Ecoregion
database_cross_reference: WWF:AA1306
database_cross_reference: https://www.worldwildlife.org/ecoregions/aa1306

Afrotropical Ecoregion
type: NamedIndividual
database_cross_reference: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Succulent Karoo Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1322
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1322

Yemen and Saudi Arabia Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1321
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1321

Yemen, Saudi Arabia, and Oman Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1320
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1320

Somali Montane Xeric Woodland Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1319
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1319

Socotran Archipelago Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1318
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1318

Red Sea Coastal Desert Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1317
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1317

Namibian Savanna Woodland Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1316
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1316

Namib Desert Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1315
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1315

Nama Karoo Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1314
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1314

Masai Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1313
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1313

Madagascar Succulent Woodlands Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1312
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1312

Madagascar Spiny Thickets Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1311
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1311

Kaokoveld Desert Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1310
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1310

Kalahari Xeric Savanna Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1309
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1309

Ile Europa and Bassas da India Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1308
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1308

Hobyo Grassland and Shrubland Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1307
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1307

Oman and United Arab Emirates Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1306
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1306

Ethiopian Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1305
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1305

Eritrean Coastal Desert Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1304
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1304

East Saharan Montane Xeric Woodland Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1303
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1303

Oman, Yemen, and Saudi Arabia Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1302
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1302

Aldabra Island Xeric Scrub Ecoregion
type: NamedIndividual
is part of: Afrotropical Ecoregion
database_cross_reference: WWF:AT1301
database_cross_reference: https://www.worldwildlife.org/ecoregions/at1301

Indo-Malay Ecoregion
type: NamedIndividual
database_cross_reference: deserts-and-xeric-shrublands

Thar Desert
type: NamedIndividual
is part of: Indo-Malay Ecoregion
database_cross_reference: im1304
database_cross_reference: WWF:IM1304

Northwestern Thorn Scrub Forests
type: NamedIndividual
is part of: Indo-Malay Ecoregion
database_cross_reference: im1303
database_cross_reference: WWF:IM1303

Solar radiation
type: NamedIndividual
process has causal agent: Q525
definition: Stellar radiation emitted from Sol.

exploratory term
type: NamedIndividual
type: data about an ontology part

exemplar term
type: NamedIndividual
type: data about an ontology part

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred label: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
term editor: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
editor preferred label: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
editor preferred label: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release
definition: The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
term editor: PERSON:Alan Ruttenberg

ready for release
type: NamedIndividual
type: curation status specification
editor preferred label: ready for release
has curation status: pending final vetting
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
type: curation status specification
editor preferred label: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
editor preferred label: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred label: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

obsolete_core
type: NamedIndividual
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: terms merged
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: term imported
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: term split
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

universal
type: NamedIndividual
type: denotator type
editor preferred label: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
term editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
editor preferred label: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
term editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
editor preferred label: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
term editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
editor preferred label: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred label: requires discussion
has curation status: pending final vetting
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

Transformation-ML
type: NamedIndividual
type: data format specification
editor preferred label: Transformation-ML
example of usage: Transformation-ML file describing parameter transformations used in a GvHD experiment.
has curation status: pending final vetting
definition: Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
term editor: person:Jennifer Fostel

ACS
type: NamedIndividual
type: data format specification
editor preferred label: ACS
example of usage: d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
has curation status: pending final vetting
definition: ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.isac-net.org/content/view/607/150/

XML
type: NamedIndividual
type: data format specification
editor preferred label: XML
example of usage: RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
has curation status: pending final vetting
definition: XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/XML/

RDF
type: NamedIndividual
type: data format specification
editor preferred label: RDF
example of usage: A FOAF file, a SKOS file, an OWL file.
has curation status: pending final vetting
definition: RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/RDF/

zip
type: NamedIndividual
type: data format specification
editor preferred label: zip
example of usage: MagicDraw MDZIP archive, Java JAR file.
has curation status: pending final vetting
definition: zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/

tar
type: NamedIndividual
type: data format specification
editor preferred label: tar
example of usage: Example.tar file.
has curation status: pending final vetting
definition: tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.gnu.org/software/tar/manual/

FCS
type: NamedIndividual
type: data format specification
editor preferred label: FCS
example of usage: d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
has curation status: pending final vetting
definition: FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.fcspress.com/

Compensation-ML
type: NamedIndividual
type: data format specification
editor preferred label: Compensation-ML
example of usage: compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
has curation status: pending final vetting
definition: Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
term editor: person:Jennifer Fostel

Gating-ML
type: NamedIndividual
type: data format specification
editor preferred label: Gating-ML
example of usage: foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
has curation status: pending final vetting
definition: Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.flowcyt.org/gating/

OWL
type: NamedIndividual
type: data format specification
editor preferred label: OWL
example of usage: OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
has curation status: pending final vetting
definition: OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
term editor: person:Jennifer Fostel
definition source: web-page:http://www.w3.org/2004/OWL/

Affymetrix
type: NamedIndividual
type: manufacturer
type: material supplier
editor preferred label: Affymetrix
example of usage: Affymetrix supplied microarray
has curation status: metadata incomplete
definition: An organization which supplies technology, tools and protocols for use in high throughput applications

Thermo
type: NamedIndividual
type: manufacturer
editor preferred label: Thermo
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Waters
type: NamedIndividual
type: manufacturer
editor preferred label: Waters
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

BIO-RAD
type: NamedIndividual
type: manufacturer
editor preferred label: BIO-RAD
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern hierarchical clustering
type: NamedIndividual
type: hierarchical clustering
editor preferred label: GenePattern hierarchical clustering
has curation status: metadata incomplete
term editor: James Malone

Ambion
type: NamedIndividual
type: manufacturer
editor preferred label: Ambion
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Helicos
type: NamedIndividual
type: manufacturer
editor preferred label: Helicos
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Roche
type: NamedIndividual
type: manufacturer
editor preferred label: Roche
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Illumina
type: NamedIndividual
type: manufacturer
editor preferred label: Illumina
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern PCA
type: NamedIndividual
type: principal components analysis dimensionality reduction
editor preferred label: GenePattern PCA
has curation status: metadata incomplete

GenePattern module SVM
type: NamedIndividual
type: GenePattern software
is about: GenePattern SVM
editor preferred label: GenePattern module SVM
has curation status: metadata incomplete
definition: GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
term editor: James Malone
term editor: Ryan Brinkman

GenePattern k-nearest neighbors
type: NamedIndividual
type: k-nearest neighbors
editor preferred label: GenePattern k-nearest neighbors
has curation status: metadata incomplete
term editor: James Malone

GenePattern LOOCV
type: NamedIndividual
type: leave one out cross validation method
editor preferred label: GenePattern LOOCV
has curation status: metadata incomplete

GenePattern k-means clustering
type: NamedIndividual
type: k-means clustering
editor preferred label: GenePattern k-means clustering
has curation status: metadata incomplete
term editor: James Malone

Agilent
type: NamedIndividual
type: manufacturer
editor preferred label: Agilent
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module KMeansClustering
type: NamedIndividual
type: GenePattern software
is about: GenePattern k-means clustering
editor preferred label: GenePattern module KMeansClustering
has curation status: metadata complete
definition: GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern CART
type: NamedIndividual
type: CART
editor preferred label: GenePattern CART
has curation status: metadata incomplete
term editor: James Malone

GenePattern module CARTXValidation
type: NamedIndividual
type: GenePattern software
is about: GenePattern LOOCV
is about: GenePattern CART
editor preferred label: GenePattern module CARTXValidation
has curation status: metadata incomplete
definition: GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.

Li-Cor
type: NamedIndividual
type: manufacturer
editor preferred label: Li-Cor
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

Bruker Corporation
type: NamedIndividual
type: manufacturer
editor preferred label: Bruker Corporation
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module KNNXValidation
type: NamedIndividual
type: GenePattern software
editor preferred label: GenePattern module KNNXValidation
has curation status: metadata complete
definition: GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern module PeakMatch
type: NamedIndividual
type: GenePattern software
is about: GenePattern peak matching
editor preferred label: GenePattern module PeakMatch
has curation status: metadata incomplete

GenePattern module KNN
type: NamedIndividual
type: GenePattern software
is about: GenePattern k-nearest neighbors
editor preferred label: GenePattern module KNN
has curation status: metadata incomplete
definition: GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
term editor: James Malone

GenePattern module HierarchicalClustering
type: NamedIndividual
type: GenePattern software
is about: GenePattern hierarchical clustering
editor preferred label: GenePattern module HierarchicalClustering
has curation status: metadata incomplete
definition: GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
term editor: James Malone
term editor: PERSON: James Malone

GenePattern SVM
type: NamedIndividual
type: support vector machine
editor preferred label: GenePattern SVM
has curation status: metadata incomplete
term editor: James Malone

Applied Biosystems
type: NamedIndividual
type: manufacturer
editor preferred label: Applied Biosystems
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern module PCA
type: NamedIndividual
type: GenePattern software
is about: GenePattern PCA
editor preferred label: GenePattern module PCA
has curation status: metadata complete
definition: GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
term editor: James Malone
definition source: PERSON: James Malone

GenePattern peak matching
type: NamedIndividual
type: peak matching
editor preferred label: GenePattern peak matching
has curation status: metadata incomplete
term editor: James Malone
term editor: Ryan Brinkman

Bruker Daltonics
type: NamedIndividual
type: manufacturer
editor preferred label: Bruker Daltonics
has curation status: metadata incomplete
term editor: Philippe Rocca-Serra

GenePattern HeatMapViewer data visualization
type: NamedIndividual
type: clustered data visualization
editor preferred label: GenePattern HeatMapViewer data visualization
has curation status: metadata incomplete
definition: The GenePattern process of generating Heat Maps from clustered data.
term editor: James Malone

GenePattern HierarchicalClusteringViewer data visualization
type: NamedIndividual
type: clustered data visualization
editor preferred label: GenePattern HierarchicalClusteringViewer data visualization
has curation status: metadata incomplete
definition: The GenePattern process of generating hierarchical clustering visualization from clustered data.
term editor: James Malone

GenePattern module HeatMapViewer
type: NamedIndividual
type: GenePattern software
is about: GenePattern HeatMapViewer data visualization
editor preferred label: GenePattern module HeatMapViewer
has curation status: metadata incomplete
definition: A GenePattern software module which is used to generate a heatmap view of data.
term editor: James Malone

GenePattern module HierarchicalClusteringViewer
type: NamedIndividual
type: GenePattern software
is about: GenePattern HierarchicalClusteringViewer data visualization
editor preferred label: GenePattern module HierarchicalClusteringViewer
has curation status: metadata incomplete
definition: A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
term editor: James Malone

Sysmex Corporation, Kobe, Japan
type: NamedIndividual
type: manufacturer
editor preferred label: Sysmex Corporation, Kobe, Japan
has curation status: metadata complete
definition source: WEB:http://www.sysmex.com/@2009/08/06

U.S. Food and Drug Administration
type: NamedIndividual
type: regulatory agency
editor preferred label: U.S. Food and Drug Administration
has curation status: metadata incomplete
alternative label: FDA

right handed
type: NamedIndividual
type: categorical label
editor preferred label: right handed
has curation status: metadata incomplete

ambidexterous
type: NamedIndividual
type: categorical label
editor preferred label: ambidexterous
has curation status: metadata incomplete

left handed
type: NamedIndividual
type: categorical label
editor preferred label: left handed
has curation status: metadata incomplete

Edingburgh handedness inventory
type: NamedIndividual
type: questionnaire
editor preferred label: Edingburgh handedness inventory
has curation status: metadata complete
definition: The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

eBioscience
type: NamedIndividual
type: manufacturer
editor preferred label: eBioscience
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.ebioscience.com/@2011/04/11

Cytopeia
type: NamedIndividual
type: manufacturer
editor preferred label: Cytopeia
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.cytopeia.com/@2011/04/11

Exalpha Biological
type: NamedIndividual
type: manufacturer
editor preferred label: Exalpha Biological
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.exalpha.com/@2011/04/11

Apogee Flow Systems
type: NamedIndividual
type: manufacturer
editor preferred label: Apogee Flow Systems
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.apogeeflow.com/@2011/04/11

Exbio Antibodies
type: NamedIndividual
type: manufacturer
editor preferred label: Exbio Antibodies
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.exbio.cz/@2011/04/11

Becton Dickinson (BD Biosciences)
type: NamedIndividual
type: manufacturer
editor preferred label: Becton Dickinson (BD Biosciences)
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.bdbiosciences.com/@2011/04/11

Dako Cytomation
type: NamedIndividual
type: manufacturer
editor preferred label: Dako Cytomation
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.dakousa.com/@2011/04/11

Millipore
type: NamedIndividual
type: manufacturer
editor preferred label: Millipore
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.guavatechnologies.com/@2011/04/11

Antigenix
type: NamedIndividual
type: manufacturer
editor preferred label: Antigenix
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.antigenix.com/@2011/04/11

Partec
type: NamedIndividual
type: manufacturer
editor preferred label: Partec
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.partec.de/@2011/04/11

Beckman Coulter
type: NamedIndividual
type: manufacturer
editor preferred label: Beckman Coulter
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.beckmancoulter.com/@2011/04/11

Advanced Instruments Inc. (AI Companies)
type: NamedIndividual
type: manufacturer
editor preferred label: Advanced Instruments Inc. (AI Companies)
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.aicompanies.com/@2011/04/11

Miltenyi Biotec
type: NamedIndividual
type: manufacturer
editor preferred label: Miltenyi Biotec
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.miltenyibiotec.com/@2011/04/11

AES Chemunex
type: NamedIndividual
type: manufacturer
editor preferred label: AES Chemunex
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.aeschemunex.com/@2011/04/11

Bentley Instruments
type: NamedIndividual
type: manufacturer
editor preferred label: Bentley Instruments
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://bentleyinstruments.com/@2011/04/11

Invitrogen
type: NamedIndividual
type: manufacturer
editor preferred label: Invitrogen
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.invitrogen.com/@2011/04/11

Luminex
type: NamedIndividual
type: manufacturer
editor preferred label: Luminex
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.luminexcorp.com/@2011/04/11

CytoBuoy
type: NamedIndividual
type: manufacturer
editor preferred label: CytoBuoy
has curation status: metadata incomplete
term editor: Karin Breuer
definition source: WEB:http://www.cytobuoy.com/@2011/04/11

Nimblegen
type: NamedIndividual
type: manufacturer
editor preferred label: Nimblegen
has curation status: metadata incomplete
definition: An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
term editor: Person: Jie Zheng

Pacific Biosciences
type: NamedIndividual
type: manufacturer
editor preferred label: Pacific Biosciences
has curation status: metadata incomplete
definition: An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
term editor: Person: Jie Zheng

NanoString Technologies
type: NamedIndividual
type: manufacturer
editor preferred label: NanoString Technologies
has curation status: metadata incomplete
definition: An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.

Thermo Fisher Scientific
type: NamedIndividual
type: organization
editor preferred label: Thermo Fisher Scientific
has curation status: metadata complete
definition: An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific

G1: Well differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G1: Well differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G1
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G2: Moderately differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G2: Moderately differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G2
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G3: Poorly differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G3: Poorly differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G3
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G4: Undifferentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G4: Undifferentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G4
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G1 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G1 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G2 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G3 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G4 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Grade 4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Low grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: Low grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Low grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

High grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: High grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
term editor: Chris Stoeckert, Helena Ellis
alternative label: High grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G1 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G1 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G2 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G3 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G4 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
term editor: Chris Stoeckert, Helena Ellis
alternative label: G4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pT0 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT0 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pTis (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pTis (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT1 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT1 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT2 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT2 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT3 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT3 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4a (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4a (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4b (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4b (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT0 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT0 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pTis (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pTis (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT3 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT3 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT4 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT4 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT0 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT0 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3c (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3c (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT4 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT4 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT0 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT0 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pN0 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN0 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1c (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1c (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN0 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN0 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN1 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN1 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN2 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN2 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN3 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN3 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN0 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN0 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN1 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN1 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN0 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN0 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

pN1 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN1 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

cM0 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM0 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM0 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM0 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM0 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM0 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

pM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: pM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM0 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM0 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

cM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

pM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: pM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
term editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

Occult Carcinoma (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Occult Carcinoma (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Occult Carcinoma
definition source: http://www.medilexicon.com/dictionary/14371
ontology term requester: NCI BBRB

Stage 0 (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage 0 (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 0
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage I (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage I (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage I
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IB2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage 1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 1C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 2C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 3C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 4 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 4 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage 4
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage Unknown (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage Unknown (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
term editor: Chris Stoeckert, Helena Ellis
alternative label: Stage Unknown
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

3: symptomatic in bed more than 50% of the day but not bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 3: symptomatic in bed more than 50% of the day but not bed ridden
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

2: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 2: symptomatic but in bed less than 50% of the day
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

4: bed ridden
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 4: bed ridden
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

0: asymptomatic
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 0: asymptomatic
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

1: symptomatic but fully ambulatory
type: NamedIndividual
type: Eastern Cooperative Oncology Group score value specification
editor preferred label: 1: symptomatic but fully ambulatory
has curation status: metadata complete
definition: An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

100: asymptomatic
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 100: asymptomatic
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is asymptomatic.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

80-90: symptomatic but fully ambulatory
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 80-90: symptomatic but fully ambulatory
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

60-70: symptomatic but in bed less than 50% of the day
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 60-70: symptomatic but in bed less than 50% of the day
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
type: NamedIndividual
type: Karnofsky score vaue specification
editor preferred label: 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
has curation status: metadata complete
definition: A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
term editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Oxford Nanopore Technologies
type: NamedIndividual
type: manufacturer
editor preferred label: Oxford Nanopore Technologies
has curation status: metadata complete
definition: An organization that is developing and selling nanopore sequencing products and is based in the UK.
term editor: James A. Overton
definition source: https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies

BioGents
type: NamedIndividual
type: manufacturer
editor preferred label: BioGents
has curation status: metadata complete
definition: An organization that manufactures mosquito traps and other mosquito control products.
term editor: John Judkins
definition source: WEB:https://eu.biogents.com/about-biogents/

out of scope
type: NamedIndividual
type: obsolescence reason specification
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
term editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
ontology term requester: https://orcid.org/0000-0001-5208-3432

meter
type: NamedIndividual
type: length unit
editor preferred label: meter
definition: A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
alternative label: m
imported from: uo.owl

kilogram
type: NamedIndividual
type: mass unit
editor preferred label: kilogram
definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
alternative label: kg
imported from: uo.owl

second
type: NamedIndividual
type: time unit
editor preferred label: second
definition: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
alternative label: s
alternative label: sec
imported from: uo.owl

centimeter
type: NamedIndividual
type: length unit
editor preferred label: centimeter
definition: A length unit which is equal to one hundredth of a meter or 10^[-2] m.
alternative label: cm
imported from: uo.owl

millimeter
type: NamedIndividual
type: length unit
editor preferred label: millimeter
definition: A length unit which is equal to one thousandth of a meter or 10^[-3] m.
alternative label: mm
imported from: uo.owl

micrometer
type: NamedIndividual
type: length unit
editor preferred label: micrometer
definition: A length unit which is equal to one millionth of a meter or 10^[-6] m.
alternative label: um
imported from: uo.owl

nanometer
type: NamedIndividual
type: length unit
editor preferred label: nanometer
definition: A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
alternative label: nm
imported from: uo.owl

angstrom
type: NamedIndividual
type: length unit
editor preferred label: angstrom
definition: A length unit which is equal to 10 [-10] m.
imported from: uo.owl

gram
type: NamedIndividual
type: mass unit
editor preferred label: gram
definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
alternative label: g
imported from: uo.owl

milligram
type: NamedIndividual
type: mass unit
editor preferred label: milligram
definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
alternative label: mg
imported from: uo.owl

microgram
type: NamedIndividual
type: mass unit
editor preferred label: microgram
definition: A mass unit which is equal to one millionth of a gram or 10^[-6] g.
alternative label: ug
imported from: uo.owl

nanogram
type: NamedIndividual
type: mass unit
editor preferred label: nanogram
definition: A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
alternative label: ng
imported from: uo.owl

picogram
type: NamedIndividual
type: mass unit
editor preferred label: picogram
definition: A mass unit which is equal to 10^[-12] g.
alternative label: pg
imported from: uo.owl

degree Celsius
type: NamedIndividual
type: temperature unit
editor preferred label: degree Celsius
definition: A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
alternative label: C
alternative label: degree C
imported from: uo.owl

minute
type: NamedIndividual
type: time unit
editor preferred label: minute
definition: A time unit which is equal to 60 seconds.
alternative label: min
imported from: uo.owl

hour
type: NamedIndividual
type: time unit
editor preferred label: hour
definition: A time unit which is equal to 3600 seconds or 60 minutes.
alternative label: h
alternative label: hr
imported from: uo.owl

day
type: NamedIndividual
type: time unit
editor preferred label: day
definition: A time unit which is equal to 24 hours.
imported from: uo.owl

week
type: NamedIndividual
type: time unit
editor preferred label: week
definition: A time unit which is equal to 7 days.
imported from: uo.owl

month
type: NamedIndividual
type: time unit
editor preferred label: month
definition: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
imported from: uo.owl

year
type: NamedIndividual
type: time unit
editor preferred label: year
definition: A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
imported from: uo.owl

micromole
type: NamedIndividual
type: substance unit
editor preferred label: micromole
definition: A substance unit equal to a millionth of a mol or 10^[-6] mol.
alternative label: umol
imported from: uo.owl

nanomole
type: NamedIndividual
type: substance unit
editor preferred label: nanomole
definition: A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
alternative label: nmol
imported from: uo.owl

picomole
type: NamedIndividual
type: substance unit
editor preferred label: picomole
definition: A substance unit equal to 10^[-12] mol.
alternative label: pmol
imported from: uo.owl

molar
type: NamedIndividual
type: concentration unit
editor preferred label: molar
definition: A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
alternative label: M
imported from: uo.owl

millimolar
type: NamedIndividual
type: concentration unit
editor preferred label: millimolar
definition: A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
alternative label: mM
imported from: uo.owl

micromolar
type: NamedIndividual
type: concentration unit
editor preferred label: micromolar
definition: A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
alternative label: uM
imported from: uo.owl

nanomolar
type: NamedIndividual
type: concentration unit
editor preferred label: nanomolar
definition: A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
alternative label: nM
imported from: uo.owl

picomolar
type: NamedIndividual
type: concentration unit
editor preferred label: picomolar
definition: A unit of molarity which is equal to 10^[-12] M.
alternative label: pM
imported from: uo.owl

cubic centimeter
type: NamedIndividual
type: volume unit
editor preferred label: cubic centimeter
definition: A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
alternative label: cc
imported from: uo.owl

milliliter
type: NamedIndividual
type: volume unit
editor preferred label: milliliter
definition: A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
alternative label: ml
imported from: uo.owl

liter
type: NamedIndividual
type: volume unit
editor preferred label: liter
definition: A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
alternative label: L
imported from: uo.owl

cubic decimeter
type: NamedIndividual
type: volume unit
editor preferred label: cubic decimeter
definition: A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
imported from: uo.owl

microliter
type: NamedIndividual
type: volume unit
editor preferred label: microliter
definition: A volume unit which is equal to one millionth of a liter or 10^[-6] L.
alternative label: ul
imported from: uo.owl

nanoliter
type: NamedIndividual
type: volume unit
editor preferred label: nanoliter
definition: A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
alternative label: nl
imported from: uo.owl

picoliter
type: NamedIndividual
type: volume unit
editor preferred label: picoliter
definition: A volume unit which is equal to 10^[-12] L.
alternative label: pl
imported from: uo.owl

hertz
type: NamedIndividual
type: frequency unit
editor preferred label: hertz
definition: A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
imported from: uo.owl

mass percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass percentage
definition: A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
alternative label: % w/w
alternative label: percent weight pr weight
imported from: uo.owl

mass volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass volume percentage
definition: A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
alternative label: % w/v
alternative label: percent vol per vol
imported from: uo.owl

volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: volume percentage
definition: A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
alternative label: % v/v
alternative label: percent vol per vol
imported from: uo.owl

gram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: gram per liter
definition: A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
alternative label: g per L
alternative label: g/L
imported from: uo.owl

milligram per milliliter
type: NamedIndividual
type: concentration unit
editor preferred label: milligram per milliliter
definition: A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
alternative label: mg per ml
alternative label: mg/ml
imported from: uo.owl

degree Fahrenheit
type: NamedIndividual
type: temperature unit
editor preferred label: degree Fahrenheit
definition: A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
imported from: uo.owl

pH
type: NamedIndividual
type: concentration unit
editor preferred label: pH
definition: A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
imported from: uo.owl

milliliter per liter
type: NamedIndividual
type: concentration unit
editor preferred label: milliliter per liter
definition: A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
alternative label: ml per L
alternative label: ml/l
imported from: uo.owl

gram per deciliter
type: NamedIndividual
type: concentration unit
editor preferred label: gram per deciliter
definition: A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
alternative label: g/dl
imported from: uo.owl

colony forming unit per volume
type: NamedIndividual
type: concentration unit
editor preferred label: colony forming unit per volume
definition: A concentration unit which a measure of viable bacterial numbers in a given volume.
imported from: uo.owl

microliters per minute
type: NamedIndividual
type: volumetric flow rate unit
editor preferred label: microliters per minute
definition: A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
imported from: uo.owl

count per nanomolar second
type: NamedIndividual
type: rate unit
editor preferred label: count per nanomolar second
definition: A rate unit which is equal to one over one nanomolar second.
imported from: uo.owl

count per molar second
type: NamedIndividual
type: rate unit
editor preferred label: count per molar second
definition: A rate unit which is equal to one over one molar second.
imported from: uo.owl

count per nanomolar
type: NamedIndividual
type: rate unit
editor preferred label: count per nanomolar
definition: A rate unit which is equal to one over one nanomolar.
imported from: uo.owl

count per molar
type: NamedIndividual
type: rate unit
editor preferred label: count per molar
definition: A rate unit which is equal to one over one molar.
imported from: uo.owl

microgram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: microgram per liter
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
alternative label: ng/ml
alternative label: ug/L
imported from: uo.owl

Axiom
annotated source: Restriction
  on property: is part of
  some values from: sequence_alteration
  subclass of: sequence_alteration
annotated property: subClassOf
annotated target: sequence_alteration
comment: Initially created such that integrated transgene infers as child of sequence_alteration.

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in