never in taxon
type: AnnotationProperty
definition source: PMID:17921072
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
expand assertion to: ?X DisjointWith RO_0002162 some ?Y
definition editor: Chris Mungall
definition source: PMID:20973947
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.

shorthand
type: AnnotationProperty

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

definition
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
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 preferred term: definition
has curation status: ready for release

expand expression to
type: AnnotationProperty
definition editor: Chris Mungall
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
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)"
editor preferred term: expand expression to

editor note
type: AnnotationProperty
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.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: ready for release

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

has curation status
type: AnnotationProperty
definition source: OBI_0000281
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
editor preferred term: has curation status

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

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: definition source
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
has curation status: ready for release

antisymmetric property
type: AnnotationProperty
definition editor: Alan Ruttenberg
editor preferred term: 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

OBO foundry unique label
type: AnnotationProperty
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 .
definition: An alternative name for a class or property which is unique across the OBO Foundry.
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
editor preferred term: OBO foundry unique label
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
has curation status: pending final vetting

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

definition editor
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition editor: PERSON:Daniel Schober
editor preferred term: definition editor
has curation status: ready for release

has obsolescence reason
type: AnnotationProperty
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
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.
editor preferred term: has obsolescence reason

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
definition editor: Chris Mungall
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)"
editor preferred term: expand assertion to

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: alternative term
has curation status: pending final vetting

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

example of usage
type: AnnotationProperty
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: example
has curation status: ready for release

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

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

part of
type: ObjectProperty
type: TransitiveProperty
shorthand: part_of
imported from: BFO
inverse of: has part
sub property of: overlaps

has part
type: ObjectProperty
type: TransitiveProperty
shorthand: has_part
imported from: BFO
sub property of: overlaps

inheres in
type: ObjectProperty
type: FunctionalProperty
shorthand: inheres_in
alternative term: inheres_in
range: independent continuant
inverse of: is bearer of

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of
domain: independent continuant

is realized by
type: ObjectProperty
alternative term: realized by
alternative term: realized_by

realizes
type: ObjectProperty
domain: process
inverse of: is realized by

participates in
type: ObjectProperty
shorthand: participates_in
alternative term: participates_in
range: occurrent
domain: independent continuant

has participant
type: ObjectProperty
shorthand: has_participant
alternative term: has_participant
range: continuant
domain: process
inverse of: participates in
property chain axiom: realizes
property chain axiom: inheres in

is preceded by
type: ObjectProperty
type: TransitiveProperty
alternative term: preceded by
alternative term: preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
range: process
domain: process
inverse of: is preceded by

occurs in
type: ObjectProperty
shorthand: occurs_in
alternative term: occurs_in
range: independent continuant
domain: process
inverse of: has site of
property chain axiom: part of

has site of
type: ObjectProperty
alternative term: has_site_of

in neural circuit with
type: ObjectProperty
type: TransitiveProperty
first order logic expression: (forall (?x ?y) (iff (neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (or (synapsed_by ?x ?y) (synapsed_to ?x ?y))))) (forall (...s ?x ?y ?z) (iff (neural_circuit_path ...s ?x ?y ?z) (and (neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (or (synapsed_by ?y ?z) (synapsed_to ?y ?z))))) (forall (?x ?y) (iff (in_neural_circuit_with ?x ?y) (exists (...s) (neural_circuit_path ?x ...s ?y))))
definition: A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
definition editor: David Osumi-Sutherland
has curation status: pending final vetting

upstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
first order logic expression: (forall (?x ?y) (iff (upstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_to ?x ?y)))) (forall (...s ?x ?y ?z) (iff (upstream_neural_circuit_path ...s ?x ?y ?z ) (and (upstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_to ?y ?z)))) (forall (?x ?y) (iff (upstream_in_neural_circuit_with ?x ?y) (exists (...s) (upstream_neural_circuit_path ?x ...s ?y))))
definition: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
definition editor: David Osumi-Sutherland
has curation status: pending final vetting
sub property of: in neural circuit with

downstream in neural circuit with
type: ObjectProperty
type: TransitiveProperty
first order logic expression: (forall (?x ?y) (iff (downstream_neural_circuit_path ?x ?y) (and ("neuron ; CL_0000540" ?x) ("neuron ; CL_0000540" ?y) (synapsed_by ?x ?y)))) (forall (...s ?x ?y ?z) (iff (downstream_neural_circuit_path ...s ?x ?y ?z ) (and (downstream_neural_circuit_path ...s ?x ?y) ("neuron ; CL_0000540" ?z) (synapsed_by ?y ?z)))) (forall (?x ?y) (iff (downstream_in_neural_circuit_with ?x ?y) (exists (...s) (downstream_neural_circuit_path ?x ...s ?y))))
definition: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
definition editor: David Osumi-Sutherland
has curation status: pending final vetting
sub property of: in neural circuit with

derives from
type: ObjectProperty
comment: Original def from OBO_REL: instance level derives_from holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later
has curation status: pending final vetting
sub property of: topObjectProperty

capable of part of
type: ObjectProperty
definition: x capable of part of Y if and only if x is the bearer or some dependent continuant that is realized by only part of some Y
expand expression to: BFO_0000053 some (BFO_0000054 only (BFO_0000050 some ?Y))
property chain axiom: capable of
property chain axiom: part of

aligned with
type: ObjectProperty
type: TransitiveProperty
has curation status: pending final vetting

has function in part of
type: ObjectProperty
definition: x has function in part of Y if and only if x is the bearer or some function that is realized by only part of some Y
expand expression to: BFO_0000053 some (BFO_0000034 that BFO_0000054 only (BFO_0000050 some ?Y))
sub property of: capable of part of
property chain axiom: has function in
property chain axiom: part of

has soma location
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
definition: Relation between a neuron and an anatomical structure that its soma is part of.
editor preferred term: soma part of
domain: neuron
has curation status: pending final vetting
sub property of: overlaps
property chain axiom: part of

fasciculates with
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
alternative term: fasciculates with
definition: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
range: neuron projection bundle
has curation status: pending final vetting
sub property of: overlaps
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

axon synapses in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure its axon forms (chemical) synapses in.
domain: neuron
has curation status: pending final vetting
sub property of: has presynaptic terminal in
property chain axiom: part of

synapsed by
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
has curation status: pending final vetting
sub property of: upstream in neural circuit with
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

has plasma membrane part
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Chris Mungall
example of usage: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
definition: Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
definition source: PMID:19243617
sub property of: has part
has curation status: pending final vetting

has postsynaptic terminal in
type: ObjectProperty
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
alternative term: synapsed in
has curation status: pending final vetting
inverse of: axon synapses in
sub property of: has synaptic terminal in
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
property chain axiom: part of

releases neurotransmitter
type: ObjectProperty
has curation status: pending final vetting
sub property of: topObjectProperty

has presynaptic terminal in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
definition: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
alternative term: synapses in
has curation status: pending final vetting
sub property of: has synaptic terminal in
property chain axiom: part of
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

synapsed to
type: ObjectProperty
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
definition: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
has curation status: pending final vetting
sub property of: downstream in neural circuit with
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

dendrite synapsed in
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
domain: neuron
has curation status: pending final vetting
sub property of: has postsynaptic terminal in
property chain axiom: part of

has synaptic terminal in
type: ObjectProperty
definition: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
alternative term: has synapse in
expand expression to: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
definition editor: David Osumi-Sutherland
has curation status: pending final vetting
sub property of: overlaps
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
property chain axiom: part of

overlaps
type: ObjectProperty
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
has curation status: pending final vetting
sub property of: topObjectProperty
property chain axiom: part of
property chain axiom: has part

has fasciculating neuron projection
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) ))))))
definition editor: David Osumi-Sutherland
definition: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
alternative term: has fasciculating component
domain: neuron projection bundle
has curation status: pending final vetting
inverse of: fasciculates with
sub property of: overlaps
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

innervates
type: ObjectProperty
expand expression to: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
definition editor: David Osumi-Sutherland
definition: Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
domain: neuron projection bundle
has curation status: pending final vetting
sub property of: topObjectProperty
property chain axiom: part of

connected to
type: ObjectProperty
definition editor: David Osumi-Sutherland
definition: X connected_to Y if and only if X and Y share a fiat boundary.
range: independent continuant
domain: independent continuant
has curation status: pending final vetting

proper overlaps
type: ObjectProperty
first order logic expression: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
alternative term: partially overlaps
has curation status: pending final vetting
sub property of: overlaps

derived by descent from
type: ObjectProperty
type: TransitiveProperty
alternative term: ancestral_stucture_of
definition: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
alternative term: evolutionarily_descended_from
has curation status: pending final vetting
inverse of: has derived by descendant
sub property of: topObjectProperty

has derived by descendant
type: ObjectProperty
type: TransitiveProperty
has curation status: pending final vetting

shares ancestor with
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
comment: VBO calls this homologous_to
definition: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
has curation status: pending final vetting
property chain axiom: derived by descent from
property chain axiom: has derived by descendant

only in taxon
type: ObjectProperty
definition source: PMID:17921072
definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
editor note: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
definition editor: Chris Mungall
definition source: PMID:20973947
example of usage: lactation SubClassOf 'only in taxon' some 'Mammalia'
has curation status: pending final vetting
sub property of: in taxon

in taxon
type: ObjectProperty
comment: Connects a biological entity to its taxon of origin.
definition source: PMID:17921072
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, expresses.
definition editor: Jennifer Deegan
definition editor: Chris Mungall
definition source: PMID:20973947
domain: entity
range: independent continuant
has curation status: pending final vetting
property chain axiom: has part
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: expressed in

spatially disjoint from
type: ObjectProperty
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
definition: A is spatially_disjoint_from B if and only if they have no parts in common
definition editor: Chris Mungall
has curation status: pending final vetting

has component
type: ObjectProperty
comment: For use in recording has_part with a cardinality constraint.
sub property of: has part
has curation status: pending final vetting

has phenotype
type: ObjectProperty
definition editor: Chris Mungall
definition source: PMID:20971987
definition editor: Robert Hoehndorf
domain: continuant
has curation status: pending final vetting
sub property of: topObjectProperty

phenotype of
type: ObjectProperty
type: FunctionalProperty
definition editor: Chris Mungall
definition source: PMID:20971987
definition editor: Robert Hoehndorf
has curation status: pending final vetting
inverse of: has phenotype
sub property of: topObjectProperty

develops from
type: ObjectProperty
type: TransitiveProperty
definition editor: Chris Mungall
definition editor: Melissa Haendel
definition editor: David Osumi-Sutherland
definition editor: Terry Meehan
comment: This is the transitive form of the develops from relation
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
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
sub property of: developmentally preceded by

develops into
type: ObjectProperty
type: TransitiveProperty
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition editor: Terry Meehan
has curation status: pending final vetting
inverse of: develops from
sub property of: developmentally succeeded by

gene product of
type: ObjectProperty
definition editor: Chris Mungall
definition: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
range: continuant
domain: independent continuant
has curation status: pending final vetting
sub property of: topObjectProperty

Axiom
curator note: TODO: make this more specific
annotated target: independent continuant
annotated source: gene product of
annotated property: domain

Axiom
curator note: TODO: make this more specific
annotated target: continuant
annotated source: gene product of
annotated property: range

has gene product
type: ObjectProperty
example of usage: every HOTAIR lncRNA is the gene product of some HOXC gene
definition editor: Chris Mungall
definition: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
example of usage: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
domain: continuant
range: independent continuant
has curation status: pending final vetting
inverse of: gene product of
sub property of: topObjectProperty

expressed in
type: ObjectProperty
definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
definition editor: Chris Mungall
domain: continuant
range: independent continuant
has curation status: pending final vetting
sub property of: topObjectProperty
property chain axiom: part of

Axiom
curator note: TODO: make this more specific
annotated target: independent continuant
annotated source: expressed in
annotated property: range

Axiom
curator note: TODO: make this more specific
annotated target: continuant
annotated source: expressed in
annotated property: domain

Axiom
comment: Example: if g1 is expressed in a hippocampus, and every hippocampus is part of some brain, then g1 is expressed in a brain
annotated source: expressed in
annotated property: propertyChainAxiom
annotated target: expressed in
annotated target: part of

directly develops from
type: ObjectProperty
definition editor: David Osumi-Sutherland
comment: TODO - add child relations from DOS
definition: Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y
definition editor: Chris Mungall
definition editor: has developmental precursor
definition source: FBbt
has curation status: pending final vetting
sub property of: develops from
domain: Class
  union of: multicellular anatomical structure
  union of: cell
range: Class
  union of: multicellular anatomical structure
  union of: cell

directly develops into
type: ObjectProperty
alternative term: developmental precursor of
has curation status: pending final vetting
sub property of: develops into
inverse of: directly develops from

regulates
type: ObjectProperty
definition editor: Tanya Berardini
definition: x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or exteny of y
definition editor: Chris Mungall
definition source: GO
definition editor: David Hill
domain: process
has curation status: pending final vetting
property chain axiom: part of
property chain axiom: ends with

negatively regulates
type: ObjectProperty
definition: x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x reduces the frequency, rate or exteny of y
has curation status: pending final vetting
sub property of: regulates
property chain axiom: ends with

positively regulates
type: ObjectProperty
definition: x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x increases the frequency, rate or exteny of y
has curation status: pending final vetting
sub property of: regulates
property chain axiom: ends with

has prototype
type: ObjectProperty
definition editor: Chris Mungall
example of usage: 'human p53 protein' SubClassOf some ('participates in' some 'DNA repair')
curator note: Experimental. In future there will be a formalization in which this relation is treated as a shortcut to some model logic axiom.
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
range: continuant
domain: continuant
has curation status: pending final vetting

capable of
type: ObjectProperty
definition: A relation between a material entity (such as a cell) and a process. This is a shortcut relation, translation rule for which is: capable_of P <-> bearer_of (some realized_by only P). Example: osteoclast capable of bone resorption.
expand expression to: BFO_0000053 some (BFO_0000054 only ?Y)
definition source: PMID:20123131
definition editor: Chris Mungall
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
alternative term: has function realized in
definition source: PMID:21208450
domain: independent continuant
range: process
has curation status: pending final vetting
property chain axiom: has prototype
property chain axiom: actively participates in

has function in
type: ObjectProperty
definition: x has function in Y if and only if x is the bearer or some function that is realized by only Y
alternative term: capable of part of
expand expression to: BFO_0000053 some (BFO_0000034 that BFO_0000054 only ?Y))
definition editor: Chris Mungall
has curation status: pending final vetting
sub property of: capable of

actively participates in
type: ObjectProperty
alternative term: agent in
definition: x actively participates in y if and only if x participates in y and x realizes some active role
sub property of: participates in
has curation status: pending final vetting
inverse of: has active participant

has active participant
type: ObjectProperty
alternative term: has agent
definition: x has participant y if and only if x realizes some active role that inheres in y
sub property of: has participant
has curation status: pending final vetting

surrounded by
type: ObjectProperty
definition: x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
has curation status: pending final vetting
sub property of: adjacent to

adjacent to
type: ObjectProperty
editor note: belongs in BFO?
definition: x adjacent to y if and only if x and y share a boundary
range: independent continuant
domain: independent continuant
has curation status: pending final vetting
sub property of: spatially disjoint from

surrounds
type: ObjectProperty
has curation status: pending final vetting
inverse of: surrounded by
sub property of: adjacent to

temporal relation
type: ObjectProperty
editor note: move to BFO?
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
definition source: Allen
range: occurrent
domain: occurrent
has curation status: pending final vetting

starts
type: ObjectProperty
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
sub property of: part of
has curation status: pending final vetting
sub property of: temporal relation

starts with
type: ObjectProperty
type: TransitiveProperty
alternative term: started by
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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.
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
sub property of: has part
has curation status: pending final vetting
sub property of: temporal relation
inverse of: starts

Axiom
annotated target: started by
editor note: From Allen terminology
annotated property: alternative term
annotated source: starts with

develops from part of
type: ObjectProperty
definition: x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
has curation status: pending final vetting
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: part of

develops in
type: ObjectProperty
editor note: todo - bring in containment relation from BFO
definition: x develops_in y if x is located in y whilst x is developing
definition source: EHDAA2
has curation status: pending final vetting
sub property of: developmentally preceded by

ends
type: ObjectProperty
definition: inverse of ends with
sub property of: part of
has curation status: pending final vetting
sub property of: temporal relation
inverse of: ends with

ends with
type: ObjectProperty
type: TransitiveProperty
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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.
alternative term: finished by
sub property of: has part
has curation status: pending final vetting
sub property of: temporal relation

Axiom
annotated target: finished by
editor note: From Allen terminology
annotated property: alternative term
annotated source: ends with

has start location
type: ObjectProperty
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has curation status: pending final vetting
property chain axiom: starts with
property chain axiom: occurs in

has end location
type: ObjectProperty
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has curation status: pending final vetting
property chain axiom: ends with
property chain axiom: occurs in

has input
type: ObjectProperty
sub property of: has participant
has curation status: pending final vetting

has output
type: ObjectProperty
sub property of: has participant
has curation status: pending final vetting

has developmental contribution from
type: ObjectProperty
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
sub property of: developmentally preceded by
property chain axiom: has part
property chain axiom: develops from

developmentally contributes to
type: ObjectProperty
has curation status: pending final vetting
inverse of: has developmental contribution from
sub property of: developmentally succeeded by

developmentally induced by
type: ObjectProperty
definition: t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
definition source: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
definition source: GO:0001759
definition editor: Melissa Haendel
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
has curation status: pending final vetting
sub property of: developmentally preceded by

developmentally induces
type: ObjectProperty
has curation status: pending final vetting
inverse of: developmentally induced by
sub property of: developmentally succeeded by

developmentally preceded by
type: ObjectProperty
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
curator note: In general you should not use this relation to make assertions - use one of the more specific relations below this one
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
has curation status: pending final vetting

developmentally replaces
type: ObjectProperty
definition editor: Chris Mungall
definition: x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
alternative term: replaces
has curation status: pending final vetting
sub property of: developmentally preceded by

developmentally succeeded by
type: ObjectProperty
definition: Inverse of developmentally preceded by
has curation status: pending final vetting
inverse of: developmentally preceded by

part of developmental precursor of
type: ObjectProperty
example of usage: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
has curation status: pending final vetting
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into

ubiquitously expressed in
type: ObjectProperty
editor note: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.
definition: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
has curation status: pending final vetting
sub property of: expressed in

expresses
type: ObjectProperty
definition: Inverse of 'expressed in'
has curation status: pending final vetting
inverse of: expressed in

ubiquitously expresses
type: ObjectProperty
has curation status: pending final vetting
inverse of: ubiquitously expressed in
sub property of: expresses

results in developmental progression of
type: ObjectProperty
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 miniam set of properties, but due to the way GO is currently structured we require highly specific relations to assign adequate differentiae to classes
domain: process
range: anatomical structure
has curation status: pending final vetting

Axiom
editor note: Consider adding GO-specific domain
annotated target: process
annotated source: results in developmental progression of
annotated property: domain

results in development of
type: ObjectProperty
example of usage: every flower development (GO:0009908) results in development of some flower (PO:0009046)
has curation status: pending final vetting
sub property of: results in developmental progression of

results in formation of
type: ObjectProperty
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
has curation status: pending final vetting
sub property of: results in developmental progression of

results in morphogenesis of
type: ObjectProperty
example of usage: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
has curation status: pending final vetting
sub property of: results in developmental progression of

results in maturation of
type: ObjectProperty
example of usage: ]bone maturation (GO:0070977) results_in_developmental_progression_of bone (UBERON:0001474)
has curation status: pending final vetting
sub property of: results in developmental progression of

results in disappearance of
type: ObjectProperty
example of usage: foramen ovale closure SubClassOf results in disappearance of foramen ovale
has curation status: pending final vetting
sub property of: results in developmental progression of

results in regression of
type: ObjectProperty
example of usage: every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
has curation status: pending final vetting
sub property of: results in developmental progression of

has habitat
type: ObjectProperty
example of usage: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'marine environment' (ENVO_00000569) -- http://eol.org/pages/1795/overview
definition: x 'has habitat' y if and only if: x is an organism, y is a habitat, and x is specially adapted (either naturally or via artifical selection) to living in y. Here 'living in' encompasses the majority of the animal's lifespan.
alternative term: adapted for living in
domain: material anatomical entity
range: habitat
has curation status: pending final vetting

Axiom
editor note: Use 'organism' when caro2 is released
annotated target: material anatomical entity
annotated source: has habitat
annotated property: domain

variant of
type: ObjectProperty

produces
type: ObjectProperty
definition editor: Melissa Haendel
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
domain: material entity
range: material entity
has curation status: pending final vetting
inverse of: produced by

produced by
type: ObjectProperty
definition editor: Melissa Haendel
range: material entity
domain: material entity
has curation status: pending final vetting

entity
type: Class
imported from: BFO

continuant
type: Class
subclass of: entity
imported from: BFO

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
example of usage: a surgical operation as processual context for a nosocomical infection
editor preferred term: occurrent
alternative term: perdurant
example of usage: the life of an organism
example of usage: the most interesting part of Van Gogh's life
example of usage: the spatiotemporal context occupied by a process of cellular meiosis
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
imported from: BFO

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: overlaps
  all values from: independent continuant
imported from: BFO

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: overlaps
  all values from: process
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
editor preferred term: process
example of usage: the life of an organism
example of usage: the process of cell-division
example of usage: the process of sleeping
imported from: BFO

material entity
type: Class
subclass of: independent continuant
imported from: BFO

anatomical structure
type: Class
subclass of: material anatomical entity
imported from: caro.owl

material anatomical entity
type: Class
subclass of: material entity
imported from: caro.owl

cell component
type: Class
subclass of: anatomical structure
imported from: caro.owl

multi-cell-component structure
type: Class
subclass of: anatomical structure
imported from: caro.owl

neuron projection bundle
type: Class
subclass of: multi-cell-component structure
imported from: caro.owl

multicellular anatomical structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: directly develops from
  all values from: multicellular anatomical structure
imported from: caro.owl

cell
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: directly develops from
  all values from: cell
imported from: cl.owl

neuron
type: Class
subclass of: cell
imported from: cl.owl

habitat
type: Class
subclass of: independent continuant
definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms.
imported from: envo.owl

membrane
type: Class
subclass of: cell part
imported from: go.owl

axon
type: Class
subclass of: neuron projection
imported from: go.owl

dendrite
type: Class
subclass of: neuron projection
imported from: go.owl

presynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
imported from: go.owl

cell projection
type: Class
subclass of: cell part
imported from: go.owl

neuron projection
type: Class
subclass of: cell projection
imported from: go.owl

synapse part
type: Class
subclass of: cell component
imported from: go.owl

cell part
type: Class
subclass of: cell component
imported from: go.owl

synapse
type: Class
subclass of: cell component
imported from: go.owl

postsynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
imported from: go.owl

data item
type: Class
subclass of: information content entity

information content entity
type: Class
subclass of: GenericallyDependentContinuant

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

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

obsolescence reason specification
type: Class
equivalent class: Class
  one of: other
  one of: terms merged
  one of: term imported
  one of: placeholder removed
  one of: failed exploratory term
  one of: term split
subclass of: data about an ontology part
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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 preferred term: obsolescence reason specification
has curation status: pending final vetting

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
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters
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.

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

metadata complete
type: NamedIndividual
type: curation status specification
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
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
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
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
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
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 definition editor.

core
type: NamedIndividual
type: Subset
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
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 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 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.

other
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
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.

defined class
type: NamedIndividual
type: denotator type
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.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
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

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
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.
definition editor: Alan Ruttenberg
definition source: group:OBI