definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: 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.
IAO_0000116: 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/
IAO_0000116: 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'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: BFO_0000031
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: 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.
IAO_0000116: 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/
IAO_0000116: 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'.
IAO_0000118: has_part
RO_0001900: RO_0001901
label: has_part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: 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.
IAO_0000116: 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.
IAO_0000118: is preceded by
IAO_0000118: preceded_by

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: 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.

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
domain: process
range: independent continuant
property chain axiom: part of
IAO_0000111: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
IAO_0000118: occurs_in
IAO_0000118: unfolds in
IAO_0000118: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
IAO_0000111: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: 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.
IAO_0000118: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
range: quality
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: 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.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: 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
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
domain: process
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: has_participant

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: function_of
IAO_0000118: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: 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
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: 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
IAO_0000116: 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.
IAO_0000118: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
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: characteristic of
definition: inverse of has disposition
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
IAO_0000111: is location of
IAO_0000112: my head is the location of my brain
IAO_0000112: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: location_of
RO_0001900: RO_0001901

contained in
type: ObjectProperty
inverse of: contains
domain: material entity
range: independent continuant
property chain axiom: located in
property chain axiom: part of
IAO_0000111: contained in
IAO_0000116: Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
IAO_0000116: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
IAO_0000116: Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
IAO_0000118: contained_in
RO_0001900: RO_0001901

contains
type: ObjectProperty
IAO_0000111: contains
RO_0001900: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
property chain axiom: part of
IAO_0000111: located in
IAO_0000112: my brain is located in my head
IAO_0000112: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
IAO_0000116: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
IAO_0000116: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000118: located_in
RO_0001900: RO_0001901

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
IAO_0000116: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
sub property of: mereotopologically related to
inverse of: has 2D boundary
IAO_0000112: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000118: 2D_boundary_of
IAO_0000118: boundary of
IAO_0000118: is 2D boundary of
IAO_0000118: is boundary of
IAO_0000118: surface of
RO_0001900: RO_0001901

has 2D boundary
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: immaterial entity
IAO_0000112: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
IAO_0000116: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
IAO_0000116: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: has boundary
IAO_0000118: has_2D_boundary
RO_0001900: RO_0001901

innervated_by
type: ObjectProperty
inverse of: innervates
IAO_0000117: https://orcid.org/0000-0002-7073-9172
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

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.
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

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.
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

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

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

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: David Osumi-Sutherland
IAO_0000118: <=
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: IAO_0000125
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

innervates
type: ObjectProperty
property chain axiom: part of
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000424: <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?)))
RO_0001900: RO_0001901
cites as authority: http://www.ncbi.nlm.nih.gov/pubmed/22402613

continuous with
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
domain: independent continuant
range: independent continuant
IAO_0000114: IAO_0000125
definition: X continuous_with Y if and only if X and Y share a fiat boundary.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000118: connected to
IAO_0000232: The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO_0001900: RO_0001901

only in taxon
type: ObjectProperty
sub property of: in taxon
IAO_0000112: lactation SubClassOf 'only in taxon' some 'Mammalia'
IAO_0000114: IAO_0000125
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.
IAO_0000116: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
property chain axiom: part of
property chain axiom: has part
property chain axiom: develops from
property chain axiom: capable of
property chain axiom: develops from part of
property chain axiom: has developmental contribution from
IAO_0000114: IAO_0000125
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.
IAO_0000117: 0000-0001-9227-417X
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
comment: Connects a biological entity to its taxon of origin.

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: part of
  some values from: system
range: Restriction
  on property: part of
  some values from: system
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552

attached to part of
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: biomechanically related to
property chain axiom: attached to
property chain axiom: part of
definition: a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
IAO_0000589: attached to part of (anatomical structure to anatomical structure)

Axiom
annotated source: attached to part of
annotated property: propertyChainAxiom
annotated target: attached to
annotated target: part of
RO_0002582: true

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: IAO_0000125
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.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901

develops from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
IAO_0000114: IAO_0000125
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
IAO_0000117: https://orcid.org/0000-0001-9114-8737
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228
comment: This is the transitive form of the develops from relation

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
IAO_0000114: IAO_0000125
definition: inverse of develops from
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: https://orcid.org/0000-0003-1980-3228

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
IAO_0000114: IAO_0000125
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 participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000119: FBbt
RO_0002575: develops from
comment: TODO - add child relations from DOS

directly develops into
type: ObjectProperty
sub property of: develops into
IAO_0000114: IAO_0000125
definition: inverse of directly develops from
IAO_0000118: developmental precursor of

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: ends with
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.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates

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
property chain axiom: ends with
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: starts with
IAO_0000114: IAO_0000125
definition: inverse of starts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000119: Allen

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000112: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: started by

develops from part of
type: ObjectProperty
sub property of: develops from
property chain axiom: directly develops from
property chain axiom: part of
IAO_0000114: IAO_0000125
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165

develops in
type: ObjectProperty
sub property of: developmentally preceded by
property chain axiom: directly develops from
property chain axiom: located in
IAO_0000114: IAO_0000125
definition: x develops_in y if x is located in y whilst x is developing
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: EHDAA2
IAO_0000119: Jonathan Bard, EHDAA2

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
inverse of: ends with
IAO_0000114: IAO_0000125
definition: inverse of ends with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: Chris Mungall
IAO_0000118: finished by

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
IAO_0000114: IAO_0000125
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts with process that occurs in

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
IAO_0000114: IAO_0000125
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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends with process that occurs in

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
property chain axiom: starts with
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: consumes

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: produces

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
property chain axiom: has part
property chain axiom: develops from
IAO_0000112: Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
IAO_0000114: IAO_0000125
definition: x has developmental contribution from y iff x has some part z such that z develops from y
IAO_0000117: 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: part of
IAO_0000114: IAO_0000125
definition: inverse of has developmental contribution from
IAO_0000117: 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
IAO_0000114: IAO_0000125
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
IAO_0000116: false
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: 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

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: 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
IAO_0000112: 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
IAO_0000114: IAO_0000125
definition: Inverse of developmentally preceded by
IAO_0000117: https://orcid.org/0000-0002-6601-2165

part of developmental precursor of
type: ObjectProperty
sub property of: developmentally succeeded by
property chain axiom: part of
property chain axiom: directly develops into
IAO_0000112: 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
IAO_0000114: IAO_0000125
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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.
RO_0004049: causally upstream of
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

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.
RO_0004050: causally upstream of

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: 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.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.

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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

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: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: actively involved in
IAO_0000118: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
IAO_0000112: 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.
IAO_0000118: is member of
IAO_0000118: member part of
IAO_0000119: SIO
RO_0001900: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
IAO_0000119: 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
IAO_0000117: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165

attached to
type: ObjectProperty
sub property of: connected to
sub property of: attached to part of
type: SymmetricProperty
definition: a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: attached to (anatomical structure to anatomical structure)

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
IAO_0000112: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
IAO_0000114: IAO_0000428
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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000428
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
IAO_0000114: IAO_0000428
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
IAO_0000117: 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
IAO_0000114: IAO_0000428
definition: inverse of upstream of
IAO_0000117: 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
IAO_0000114: IAO_0000428
IAO_0000117: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly activates
RO_0002579: positively regulates

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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
IAO_0000116: 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…
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

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.
IAO_0000117: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
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.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: 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
IAO_0000117: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004050: involved in regulation of

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
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: executes activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

contributes to morphology of
type: ObjectProperty
sub property of: overlaps
definition: p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.

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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: binds
IAO_0000118: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly activates

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

composed primarily of
type: ObjectProperty
sub property of: has part
domain: material entity
range: material entity
IAO_0000112: 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
definition: x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
RO_0001900: RO_0001901

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: https://orcid.org/0000-0002-6601-2165

relation between physical entity and a process or stage
type: ObjectProperty
domain: independent continuant
range: occurrent
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
definition: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence starts with
type: ObjectProperty
sub property of: existence starts during
definition: x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
definition: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
definition: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends with
type: ObjectProperty
sub property of: existence ends during
definition: x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

transformation of
type: ObjectProperty
sub property of: develops from
type: TransitiveProperty
definition: x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediate transformation of
type: ObjectProperty
sub property of: directly develops from
sub property of: transformation of
definition: x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0002575: transformation of

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally preceded by
property chain axiom: preceded by
property chain axiom: simultaneous with
definition: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: developmentally succeeded by
property chain axiom: precedes
property chain axiom: simultaneous with
definition: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

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
IAO_0000119: 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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
IAO_0000116: 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
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: 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).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
definition: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.

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.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates

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
IAO_0000112: 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
IAO_0000117: 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.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: 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.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: 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.
IAO_0000119: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

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.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates

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.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates

produces
type: ObjectProperty
inverse of: produced by
domain: material entity
range: material entity
property chain axiom:
  inverse of: occurs in
property chain axiom: has output
IAO_0000114: IAO_0000125
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.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
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.

produced by
type: ObjectProperty
domain: material entity
range: material entity
IAO_0000114: IAO_0000125
definition: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: https://orcid.org/0000-0001-9114-8737

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
RO_0004049: acts upstream of or within

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
RO_0004050: acts upstream of or within

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
RO_0004049: acts upstream of

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
RO_0004050: acts upstream of

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within

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.
IAO_0000117: 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 cross section
type: ObjectProperty
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: 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.
IAO_0000117: https://orcid.org/0000-0001-9625-1899
IAO_0000117: https://orcid.org/0000-0003-2620-0345
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497

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.

has number of atomic nuclei
type: DatatypeProperty
domain: material entity
range: nonNegativeInteger

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
IAO_0000112: Julius Caesar
IAO_0000112: Verdi’s Requiem
IAO_0000112: the Second World War
IAO_0000112: your body mass index
IAO_0000116: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
IAO_0000116: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
IAO_0000600: 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: IAO_0000116
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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: IAO_0000600
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO_0000179: continuant
BFO_0000180: 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.
IAO_0000116: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
IAO_0000116: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
IAO_0000600: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0000602: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0000602: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0000602: (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: IAO_0000116
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
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: IAO_0000602
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: 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.
IAO_0000116: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
IAO_0000116: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
IAO_0000116: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0000116: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
IAO_0000600: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
IAO_0000601: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0000601: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0000602: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0000602: (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: IAO_0000116
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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: IAO_0000116
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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000601
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: IAO_0000602
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
BFO_0000179: ic
BFO_0000180: IndependentContinuant
IAO_0000112: a chair
IAO_0000112: a heart
IAO_0000112: a leg
IAO_0000112: a molecule
IAO_0000112: a spatial region
IAO_0000112: an atom
IAO_0000112: an orchestra.
IAO_0000112: an organism
IAO_0000112: the bottom right portion of a human torso
IAO_0000112: 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])
IAO_0000601: 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])
IAO_0000601: 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])
IAO_0000602: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0000602: (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]
IAO_0000602: (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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: IAO_0000602
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
BFO_0000179: s-region
BFO_0000180: SpatialRegion
IAO_0000116: BFO 2 Reference: Spatial regions do not participate in processes.
IAO_0000116: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
IAO_0000600: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
IAO_0000601: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
IAO_0000602: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
IAO_0000602: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: IAO_0000116
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: IAO_0000600
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: IAO_0000601
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: IAO_0000602
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: IAO_0000602
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/035-001

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  all values from: process
BFO_0000179: process
BFO_0000180: Process
IAO_0000112: a process of cell-division, \ a beating of the heart
IAO_0000112: a process of meiosis
IAO_0000112: a process of sleeping
IAO_0000112: the course of a disease
IAO_0000112: the flight of a bird
IAO_0000112: the life of an organism
IAO_0000112: 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])
IAO_0000116: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
IAO_0000602: (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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable
disjoint with: role
BFO_0000179: disposition
BFO_0000180: Disposition
IAO_0000112: an atom of element X has the disposition to decay to an atom of element Y
IAO_0000112: certain people have a predisposition to colon cancer
IAO_0000112: children are innately disposed to categorize objects in certain ways.
IAO_0000112: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
IAO_0000116: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
IAO_0000600: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
IAO_0000601: 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])
IAO_0000602: (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]
IAO_0000602: (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: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable
type: Class
subclass of: specifically dependent continuant
subclass of: quality
subclass of: Restriction
  on property: part of
  all values from: realizable
disjoint with: quality
BFO_0000179: realizable
BFO_0000180: RealizableEntity
IAO_0000112: the disposition of this piece of metal to conduct electricity.
IAO_0000112: the disposition of your blood to coagulate
IAO_0000112: the function of your reproductive organs
IAO_0000112: the role of being a doctor
IAO_0000112: 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.
IAO_0000600: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
IAO_0000601: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0000602: (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]
IAO_0000602: (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]
label: realizable entity

Axiom
annotated source: realizable
annotated property: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable
annotated property: IAO_0000601
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/058-002

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality
BFO_0000179: quality
BFO_0000180: Quality
IAO_0000112: the ambient temperature of this portion of air
IAO_0000112: the color of a tomato
IAO_0000112: the length of the circumference of your waist
IAO_0000112: the mass of this piece of gold.
IAO_0000112: the shape of your nose
IAO_0000112: the shape of your nostril
IAO_0000600: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
IAO_0000601: 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])
IAO_0000602: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0000602: (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: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000601
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: IAO_0000602
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
BFO_0000179: sdc
BFO_0000180: SpecificallyDependentContinuant
IAO_0000112: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
IAO_0000112: of one-sided specifically dependent continuants: the mass of this tomato
IAO_0000112: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
IAO_0000112: the disposition of this fish to decay
IAO_0000112: the function of this heart: to pump blood
IAO_0000112: the mutual dependence of proton donors and acceptors in chemical reactions [79
IAO_0000112: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
IAO_0000112: the pink color of a medium rare piece of grilled filet mignon at its center
IAO_0000112: the role of being a doctor
IAO_0000112: the shape of this hole.
IAO_0000112: 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 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])
IAO_0000116: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
IAO_0000602: (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 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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000116
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.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable
BFO_0000179: role
BFO_0000180: Role
IAO_0000112: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
IAO_0000112: the priest role
IAO_0000112: the role of a boundary to demarcate two neighboring administrative territories
IAO_0000112: the role of a building in serving as a military target
IAO_0000112: the role of a stone in marking a property boundary
IAO_0000112: the role of subject in a clinical trial
IAO_0000112: 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.
IAO_0000116: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
IAO_0000600: 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])
IAO_0000602: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: IAO_0000602
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/061-001

function
type: Class
subclass of: disposition
BFO_0000179: function
BFO_0000180: Function
IAO_0000112: the function of a hammer to drive in nails
IAO_0000112: the function of a heart pacemaker to regulate the beating of a heart through electricity
IAO_0000112: the function of amylase in saliva to break down starch into sugar
IAO_0000116: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
IAO_0000600: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
IAO_0000602: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: IAO_0000600
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: IAO_0000602
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/064-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
BFO_0000179: material
BFO_0000180: MaterialEntity
IAO_0000112: a flame
IAO_0000112: a forest fire
IAO_0000112: a human being
IAO_0000112: a hurricane
IAO_0000112: a photon
IAO_0000112: a puff of smoke
IAO_0000112: a sea wave
IAO_0000112: a tornado
IAO_0000112: an aggregate of human beings.
IAO_0000112: an energy wave
IAO_0000112: an epidemic
IAO_0000112: 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.
IAO_0000116: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
IAO_0000116: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
IAO_0000116: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
IAO_0000600: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
IAO_0000601: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0000601: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0000602: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0000602: (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]
IAO_0000602: (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: IAO_0000600
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])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: IAO_0000601
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: IAO_0000602
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]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/020-002

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity
BFO_0000179: immaterial
BFO_0000180: ImmaterialEntity
IAO_0000116: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

electron
type: Class
subclass of: lepton
subclass of: molecular entity
subclass of: Restriction
  on property: has number of atomic nuclei
  has value: 0
definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
charge: -1
mass: 0.000548579903
monoisotopicmass: 0.0
label: nucleic acid polymer

molecular entity
type: Class
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.

chemical entity
type: Class
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.

group
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has part
  some values from: atom
definition: A defined linked collection of atoms or a single atom within a molecular entity.

fundamental particle
type: Class
subclass of: subatomic particle
definition: A particle not known to have substructure.

atom
type: Class
subclass of: chemical entity
subclass of: atom
subclass of: Restriction
  on property: has part
  some values from: electron
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
label: uncharged atom

atomic nucleus
type: Class
subclass of: nuclear particle
subclass of: Restriction
  on property: has part
  some values from: nucleon
definition: A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
comment: Some people may be uncomfortable calling every proton an atomic nucleus
comment: This is equivalent to CHEBI:33252

nucleon
type: Class
subclass of: baryon
subclass of: nuclear particle
definition: Heavy nuclear particle: proton or neutron.

macromolecule
type: Class
subclass of: polyatomic entity
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.

lepton
type: Class
subclass of: fundamental particle
subclass of: fermion
definition: Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).

baryon
type: Class
subclass of: fermion
subclass of: hadron
definition: Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).

fermion
type: Class
subclass of: subatomic particle
definition: Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.

subatomic particle
type: Class
subclass of: material entity
definition: A particle smaller than an atom.

composite particle
type: Class
subclass of: subatomic particle
definition: A subatomic particle known to have substructure (i.e. consisting of smaller particles).

hadron
type: Class
subclass of: composite particle
definition: Hadron is a subatomic particle which experiences the strong force.

nuclear particle
type: Class
subclass of: subatomic particle
definition: A nucleus or any of its constituents in any of their energy states.

polyatomic entity
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: has part
  some values from: group
definition: Any molecular entity consisting of more than one atom.

atom
type: Class
equivalent class: Restriction
  on property: has number of atomic nuclei
  has value: 1
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atomic nucleus
disjoint with: molecular entity
definition: A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
comment: This atom is closely related to ChEBI's atom, but not exactly equivalent to.

molecular entity
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atom
disjoint with: complex of molecular entities
definition: A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.
comment: This molecular entity is different than ChEBI's 'molecular entity'.
comment: We would like to have cardinality restrictions on the logic, but there are some technical limitations.

gene product
type: Class
subclass of: molecular entity

complex of molecular entities
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: molecular entity
definition: A complex of two or more molecular entities that are not covalently bound.

Axiom
annotated source: complex of molecular entities
annotated property: subClassOf
annotated target: Restriction
  on property: has part
  some values from: molecular entity
comment: >=2 parts (not we cannot use cardinality with transitive properties)

reproduction
type: Class
subclass of: biological_process

ameboidal-type cell migration
type: Class
subclass of: cell migration
comment: Note that this term refers to a mode of migration rather than to any particular cell type.

formation of primary germ layer
type: Class
subclass of: anatomical structure formation involved in morphogenesis
subclass of: Restriction
  on property: part of
  some values from: gastrulation

ectoderm formation
type: Class
subclass of: formation of primary germ layer
subclass of: Restriction
  on property: part of
  some values from: ectoderm development

endoderm formation
type: Class
subclass of: formation of primary germ layer
subclass of: Restriction
  on property: part of
  some values from: endoderm development

mesoderm formation
type: Class
subclass of: formation of primary germ layer
subclass of: Restriction
  on property: part of
  some values from: mesoderm morphogenesis

serotonin secretion
type: Class
subclass of: serotonin transport
subclass of: signal release

embryonic epithelial tube formation
type: Class
subclass of: epithelial tube formation
subclass of: Restriction
  on property: part of
  some values from: morphogenesis of embryonic epithelium

neural tube formation
type: Class
subclass of: embryonic epithelial tube formation
subclass of: Restriction
  on property: part of
  some values from: neural tube development

morphogenesis of an epithelium
type: Class
subclass of: tissue morphogenesis
subclass of: Restriction
  on property: part of
  some values from: epithelium development

regulation of respiratory gaseous exchange by nervous system process
type: Class
equivalent class: Class
  intersection of: nervous system process
  intersection of: Restriction
    on property: regulates
    some values from: respiratory gaseous exchange by respiratory system
subclass of: regulation of respiratory system process
subclass of: nervous system process

aggressive behavior
type: Class
subclass of: behavior

peptide secretion
type: Class
subclass of: peptide transport
subclass of: secretion

regulation of peptide secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: peptide secretion
subclass of: regulation of secretion
subclass of: regulation of peptide transport
subclass of: Restriction
  on property: regulates
  some values from: peptide secretion

negative regulation of peptide secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: peptide secretion
subclass of: regulation of peptide secretion
subclass of: negative regulation of secretion
subclass of: Restriction
  on property: negatively regulates
  some values from: peptide secretion

positive regulation of peptide secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: peptide secretion
subclass of: regulation of peptide secretion
subclass of: positive regulation of secretion
subclass of: Restriction
  on property: positively regulates
  some values from: peptide secretion

developmental process involved in reproduction
type: Class
equivalent class: Class
  intersection of: developmental process
  intersection of: Restriction
    on property: part of
    some values from: reproduction
subclass of: reproductive process
subclass of: developmental process

system process
type: Class
subclass of: multicellular organismal process

muscle system process
type: Class
subclass of: system process

renal system process
type: Class
subclass of: system process

respiratory system process
type: Class
subclass of: system process
subclass of: Restriction
  on property: part of
  some values from: respiratory gaseous exchange by respiratory system

molecular_function
type: Class
subclass of: process
subclass of: Restriction
  on property: enabled by
  some values from: Class
    union of: gene product
    union of: protein-containing complex
disjoint with: biological_process
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
comment: This is the same as GO molecular function
label: gene product or complex activity

catalytic activity
type: Class
subclass of: molecular_function

cellular_component
type: Class
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

intracellular anatomical structure
type: Class
subclass of: cellular anatomical entity
IAO_0000233: https://github.com/geneontology/go-ontology/issues/17776

cytoplasm
type: Class
subclass of: cellular anatomical entity
subclass of: Restriction
  on property: part of
  some values from: intracellular anatomical structure
IAO_0000233: https://github.com/geneontology/go-ontology/issues/23023

cytoskeleton
type: Class
subclass of: intracellular non-membrane-bounded organelle

plasma membrane
type: Class
subclass of: membrane
subclass of: Restriction
  on property: part of
  some values from: cell periphery

cell cortex
type: Class
equivalent class: Class
  intersection of: cytoplasm
  intersection of: Restriction
    on property: part of
    some values from: cell periphery
subclass of: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: cell periphery

carbohydrate metabolic process
type: Class
subclass of: primary metabolic process
subclass of: organic substance metabolic process
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22880

organic acid metabolic process
type: Class
subclass of: cellular metabolic process
subclass of: small molecule metabolic process
subclass of: organic substance metabolic process

generation of precursor metabolites and energy
type: Class
subclass of: cellular metabolic process

regulation of carbohydrate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: carbohydrate metabolic process
subclass of: regulation of primary metabolic process
subclass of: Restriction
  on property: regulates
  some values from: carbohydrate metabolic process

lipid metabolic process
type: Class
subclass of: primary metabolic process
subclass of: organic substance metabolic process

phosphorus metabolic process
type: Class
subclass of: cellular metabolic process

phosphate-containing compound metabolic process
type: Class
subclass of: phosphorus metabolic process

transport
type: Class
subclass of: establishment of localization
IAO_0000233: https://github.com/geneontology/go-ontology/issues/20292
comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.

monoatomic ion transport
type: Class
subclass of: transport

serotonin transport
type: Class
subclass of: monoamine transport
subclass of: organic hydroxy compound transport

lipid transport
type: Class
subclass of: organic substance transport
subclass of: Restriction
  on property: part of
  some values from: lipid localization

intracellular protein transport
type: Class
subclass of: protein transport
subclass of: intracellular transport
subclass of: Restriction
  on property: part of
  some values from: protein localization

muscle contraction
type: Class
subclass of: muscle system process

regulation of muscle contraction
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: muscle contraction
subclass of: regulation of muscle system process
subclass of: Restriction
  on property: regulates
  some values from: muscle contraction

response to stress
type: Class
subclass of: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

cell communication
type: Class
subclass of: cellular process

cell-cell signaling
type: Class
subclass of: cell communication
subclass of: signaling

multicellular organism development
type: Class
subclass of: multicellular organismal process
subclass of: anatomical structure development
IAO_0000233: https://github.com/geneontology/go-ontology/issues/21234
comment: Note that this term was 'developmental process'.

gamete generation
type: Class
subclass of: multicellular organismal reproductive process
subclass of: Restriction
  on property: part of
  some values from: sexual reproduction
RO_0002161: NCBITaxon Union 0000023

gastrulation
type: Class
subclass of: embryonic morphogenesis
subclass of: Restriction
  on property: has part
  some values from: ectoderm formation
subclass of: Restriction
  on property: has part
  some values from: endoderm formation
subclass of: Restriction
  on property: has part
  some values from: mesoderm formation

ectoderm development
type: Class
subclass of: tissue development

nervous system development
type: Class
subclass of: system development

endoderm development
type: Class
subclass of: tissue development

mesoderm development
type: Class
subclass of: tissue development

respiratory gaseous exchange by respiratory system
type: Class
subclass of: multicellular organismal process

digestion
type: Class
subclass of: multicellular organismal process

body fluid secretion
type: Class
subclass of: secretion
subclass of: regulation of body fluid levels

sensory perception
type: Class
subclass of: nervous system process

visual perception
type: Class
subclass of: sensory perception of light stimulus

sensory perception of sound
type: Class
subclass of: sensory perception of mechanical stimulus

sensory perception of chemical stimulus
type: Class
subclass of: sensory perception

sensory perception of smell
type: Class
subclass of: sensory perception of chemical stimulus

behavior
type: Class
subclass of: multicellular organismal process
disjoint with: developmental process
comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).

mating behavior
type: Class
subclass of: reproductive behavior

courtship behavior
type: Class
subclass of: mating behavior

copulation
type: Class
subclass of: mating behavior

rhythmic behavior
type: Class
subclass of: behavior

circadian rhythm
type: Class
subclass of: rhythmic process

grooming behavior
type: Class
subclass of: behavior
has exact synonym: groom

locomotory behavior
type: Class
subclass of: behavior

flight behavior
type: Class
subclass of: adult locomotory behavior
has exact synonym: fly

feeding behavior
type: Class
subclass of: behavior
IAO_0000233: https://github.com/geneontology/go-ontology/issues/18547
comment: See also the biological process term 'behavior ; GO:0007610'.

visual behavior
type: Class
subclass of: behavior
subclass of: response to light stimulus

chemosensory behavior
type: Class
subclass of: behavior
subclass of: Restriction
  on property: part of
  some values from: response to chemical

mechanosensory behavior
type: Class
subclass of: behavior
subclass of: Restriction
  on property: part of
  some values from: response to mechanical stimulus

male courtship behavior
type: Class
subclass of: courtship behavior
subclass of: male mating behavior

protein localization
type: Class
subclass of: cellular macromolecule localization
IAO_0000233: https://github.com/geneontology/go-ontology/issues/23112

biological_process
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: molecular_function
definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/24968
comment: A biological process is an evolved process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
label: biological process

metabolic process
type: Class
subclass of: biological_process
disjoint with: localization
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.

adult locomotory behavior
type: Class
subclass of: locomotory behavior
subclass of: adult behavior
comment: See also the biological process term 'locomotory behavior ; GO:0007626'.

lipid biosynthetic process
type: Class
subclass of: lipid metabolic process
subclass of: organic substance biosynthetic process

catabolic process
type: Class
subclass of: metabolic process

macromolecule catabolic process
type: Class
subclass of: macromolecule metabolic process
subclass of: organic substance catabolic process

biosynthetic process
type: Class
subclass of: metabolic process

macromolecule biosynthetic process
type: Class
subclass of: macromolecule metabolic process
subclass of: organic substance biosynthetic process
IAO_0000233: http://amigo.geneontology.org/amigo/term/GO:0070589

response to temperature stimulus
type: Class
subclass of: response to abiotic stimulus

protein secretion
type: Class
subclass of: protein transport
subclass of: secretion by cell
subclass of: establishment of protein localization to extracellular region

response to radiation
type: Class
subclass of: response to abiotic stimulus
comment: Note that 'radiation' refers to electromagnetic radiation of any wavelength.

response to light stimulus
type: Class
subclass of: response to radiation

detection of external stimulus
type: Class
subclass of: response to external stimulus
subclass of: detection of stimulus

detection of abiotic stimulus
type: Class
subclass of: response to abiotic stimulus
subclass of: detection of stimulus

detection of light stimulus
type: Class
subclass of: response to light stimulus
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus

detection of visible light
type: Class
subclass of: detection of light stimulus

detection of chemical stimulus
type: Class
subclass of: detection of stimulus
subclass of: Restriction
  on property: part of
  some values from: response to chemical

response to external stimulus
type: Class
subclass of: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

response to mechanical stimulus
type: Class
subclass of: response to external stimulus
subclass of: response to abiotic stimulus

response to abiotic stimulus
type: Class
subclass of: response to stimulus
IAO_0000233: https://github.com/geneontology/go-ontology/issues/16572
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

anatomical structure morphogenesis
type: Class
subclass of: developmental process
subclass of: Restriction
  on property: part of
  some values from: anatomical structure development

embryo development
type: Class
subclass of: multicellular organism development

post-embryonic development
type: Class
subclass of: multicellular organismal process
subclass of: Restriction
  on property: part of
  some values from: multicellular organism development

embryo development ending in birth or egg hatching
type: Class
subclass of: embryo development

tissue development
type: Class
subclass of: anatomical structure development
RO_0002161: NCBITaxon_147554
RO_0002161: NCBITaxon_33630
RO_0002161: NCBITaxon_33682
RO_0002161: NCBITaxon_38254
RO_0002161: NCBITaxon 4891

regulation of biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: biosynthetic process
subclass of: regulation of metabolic process
subclass of: Restriction
  on property: regulates
  some values from: biosynthetic process

negative regulation of biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: biosynthetic process
subclass of: regulation of biosynthetic process
subclass of: negative regulation of metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: biosynthetic process

positive regulation of biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: biosynthetic process
subclass of: regulation of biosynthetic process
subclass of: positive regulation of metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: biosynthetic process

negative regulation of metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: metabolic process
subclass of: regulation of metabolic process
subclass of: negative regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: metabolic process

positive regulation of metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: metabolic process
subclass of: regulation of metabolic process
subclass of: positive regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: metabolic process

regulation of catabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: catabolic process
subclass of: regulation of metabolic process
subclass of: Restriction
  on property: regulates
  some values from: catabolic process

negative regulation of catabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: catabolic process
subclass of: negative regulation of metabolic process
subclass of: regulation of catabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: catabolic process

positive regulation of catabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: catabolic process
subclass of: positive regulation of metabolic process
subclass of: regulation of catabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: catabolic process

hormone transport
type: Class
subclass of: transport
subclass of: regulation of hormone levels

cellular process
type: Class
subclass of: biological_process
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.

response to organic substance
type: Class
subclass of: response to chemical

response to inorganic substance
type: Class
subclass of: response to chemical

regulation of gastrulation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: gastrulation
subclass of: regulation of anatomical structure morphogenesis
subclass of: regulation of embryonic development
subclass of: Restriction
  on property: regulates
  some values from: gastrulation

regulation of macromolecule biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: macromolecule biosynthetic process
subclass of: regulation of biosynthetic process
subclass of: regulation of macromolecule metabolic process
subclass of: Restriction
  on property: regulates
  some values from: macromolecule biosynthetic process

positive regulation of macromolecule biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: macromolecule biosynthetic process
subclass of: positive regulation of biosynthetic process
subclass of: regulation of macromolecule biosynthetic process
subclass of: positive regulation of macromolecule metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: macromolecule biosynthetic process

negative regulation of macromolecule biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: macromolecule biosynthetic process
subclass of: negative regulation of biosynthetic process
subclass of: regulation of macromolecule biosynthetic process
subclass of: negative regulation of macromolecule metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: macromolecule biosynthetic process

positive regulation of phosphorus metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: phosphorus metabolic process
subclass of: positive regulation of cellular metabolic process
subclass of: regulation of phosphorus metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: phosphorus metabolic process

negative regulation of phosphorus metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: phosphorus metabolic process
subclass of: negative regulation of cellular metabolic process
subclass of: regulation of phosphorus metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: phosphorus metabolic process

regulation of cellular ketone metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular ketone metabolic process
subclass of: regulation of cellular metabolic process
subclass of: regulation of small molecule metabolic process
subclass of: Restriction
  on property: regulates
  some values from: cellular ketone metabolic process

positive regulation of macromolecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: macromolecule metabolic process
subclass of: positive regulation of metabolic process
subclass of: regulation of macromolecule metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: macromolecule metabolic process

negative regulation of macromolecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: macromolecule metabolic process
subclass of: negative regulation of metabolic process
subclass of: regulation of macromolecule metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: macromolecule metabolic process

regulation of cell communication
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cell communication
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cell communication

positive regulation of cell communication
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cell communication
subclass of: regulation of cell communication
subclass of: positive regulation of cellular process
subclass of: Restriction
  on property: positively regulates
  some values from: cell communication

negative regulation of cell communication
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cell communication
subclass of: regulation of cell communication
subclass of: negative regulation of cellular process
subclass of: Restriction
  on property: negatively regulates
  some values from: cell communication

regulation of hormone levels
type: Class
subclass of: regulation of biological quality

lipid localization
type: Class
subclass of: macromolecule localization

regulation of serotonin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: serotonin secretion
subclass of: regulation of monoatomic ion transport
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: regulates
  some values from: serotonin secretion

negative regulation of serotonin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: serotonin secretion
subclass of: regulation of serotonin secretion
subclass of: negative regulation of monoatomic ion transport
subclass of: negative regulation of secretion by cell
subclass of: Restriction
  on property: negatively regulates
  some values from: serotonin secretion

positive regulation of serotonin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: serotonin secretion
subclass of: regulation of serotonin secretion
subclass of: positive regulation of monoatomic ion transport
subclass of: positive regulation of secretion by cell
subclass of: Restriction
  on property: positively regulates
  some values from: serotonin secretion

protein transport
type: Class
subclass of: establishment of protein localization
subclass of: organic substance transport
subclass of: nitrogen compound transport

organic cation transport
type: Class
subclass of: organic substance transport

organic anion transport
type: Class
subclass of: organic substance transport

monocarboxylic acid transport
type: Class
subclass of: carboxylic acid transport

peptide transport
type: Class
subclass of: amide transport
subclass of: organic substance transport

amine transport
type: Class
subclass of: organic substance transport
subclass of: nitrogen compound transport

monoamine transport
type: Class
subclass of: organic substance transport
subclass of: nitrogen compound transport

organic acid transport
type: Class
subclass of: organic substance transport

organic hydroxy compound transport
type: Class
subclass of: organic substance transport

energy derivation by oxidation of organic compounds
type: Class
subclass of: generation of precursor metabolites and energy

membrane
type: Class
subclass of: cellular anatomical entity

cellular component organization
type: Class
subclass of: cellular component organization or biogenesis

detection of temperature stimulus
type: Class
subclass of: response to temperature stimulus
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus

carbohydrate catabolic process
type: Class
subclass of: carbohydrate metabolic process
subclass of: organic substance catabolic process

organic acid biosynthetic process
type: Class
subclass of: organic acid metabolic process
subclass of: cellular biosynthetic process
subclass of: small molecule biosynthetic process
subclass of: organic substance biosynthetic process

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

phosphorylation
type: Class
subclass of: phosphate-containing compound metabolic process

morphogenesis of embryonic epithelium
type: Class
subclass of: morphogenesis of an epithelium
subclass of: embryonic morphogenesis

cell migration
type: Class
subclass of: cell motility
IAO_0000233: https://github.com/geneontology/go-ontology/issues/24787

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.

reproductive behavior
type: Class
equivalent class: Class
  intersection of: behavior
  intersection of: Restriction
    on property: part of
    some values from: multicellular organism reproduction
subclass of: behavior
subclass of: reproductive process
subclass of: Restriction
  on property: part of
  some values from: multicellular organism reproduction
IAO_0000233: https://github.com/geneontology/go-ontology/issues/23491

regulation of lipid metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: lipid metabolic process
subclass of: regulation of primary metabolic process
subclass of: Restriction
  on property: regulates
  some values from: lipid metabolic process

regulation of phosphate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: phosphate-containing compound metabolic process
subclass of: regulation of phosphorus metabolic process
subclass of: Restriction
  on property: regulates
  some values from: phosphate-containing compound metabolic process

regulation of metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: metabolic process
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: metabolic process

sensory perception of pain
type: Class
subclass of: sensory perception

carboxylic acid metabolic process
type: Class
subclass of: oxoacid metabolic process

sexual reproduction
type: Class
subclass of: reproduction
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22929
comment: Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.

neural tube development
type: Class
subclass of: tube development
subclass of: epithelium development
subclass of: Restriction
  on property: part of
  some values from: nervous system development
subclass of: Restriction
  on property: part of
  some values from: chordate embryonic development

circadian sleep/wake cycle process
type: Class
subclass of: circadian behavior
subclass of: Restriction
  on property: part of
  some values from: circadian sleep/wake cycle

cellular process involved in reproduction in multicellular organism
type: Class
equivalent class: Class
  intersection of: cellular process
  intersection of: Restriction
    on property: part of
    some values from: multicellular organism reproduction
subclass of: cellular process
subclass of: reproductive process
subclass of: Restriction
  on property: part of
  some values from: multicellular organism reproduction

reproductive process
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: part of
    some values from: reproduction
subclass of: biological_process
subclass of: Restriction
  on property: part of
  some values from: reproduction

digestive system process
type: Class
equivalent class: Class
  intersection of: system process
  intersection of: Restriction
    on property: part of
    some values from: digestion
subclass of: system process
subclass of: Restriction
  on property: part of
  some values from: digestion

regulation of anatomical structure morphogenesis
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: anatomical structure morphogenesis
subclass of: regulation of developmental process
subclass of: Restriction
  on property: regulates
  some values from: anatomical structure morphogenesis

regulation of signaling
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: signaling
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: signaling

signaling
type: Class
subclass of: regulation of biological process
comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.

positive regulation of signaling
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: signaling
subclass of: regulation of signaling
subclass of: positive regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: signaling

negative regulation of signaling
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: signaling
subclass of: regulation of signaling
subclass of: negative regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: signaling

signal release
type: Class
equivalent class: Class
  intersection of: secretion by cell
  intersection of: Restriction
    on property: part of
    some values from: cell-cell signaling
subclass of: secretion by cell
subclass of: Restriction
  on property: part of
  some values from: cell-cell signaling

cell junction
type: Class
subclass of: cellular anatomical entity
RO_0002161: NCBITaxon 4751

peptide hormone secretion
type: Class
subclass of: peptide secretion
subclass of: hormone secretion

insulin secretion
type: Class
subclass of: protein secretion
subclass of: peptide hormone secretion
IAO_0000233: https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045

external encapsulating structure
type: Class
subclass of: cellular anatomical entity
subclass of: Restriction
  on property: part of
  some values from: cell periphery
comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.

regulation of cell migration
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cell migration
subclass of: regulation of cell motility
subclass of: Restriction
  on property: regulates
  some values from: cell migration

positive regulation of cell migration
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cell migration
subclass of: regulation of cell migration
subclass of: positive regulation of cell motility
subclass of: Restriction
  on property: positively regulates
  some values from: cell migration

negative regulation of cell migration
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cell migration
subclass of: regulation of cell migration
subclass of: negative regulation of cell motility
subclass of: Restriction
  on property: negatively regulates
  some values from: cell migration

sleep
type: Class
subclass of: multicellular organismal process

adult behavior
type: Class
subclass of: behavior
comment: See also the biological process term 'behavior ; GO:0007610'.

extracellular matrix
type: Class
subclass of: external encapsulating structure

organelle membrane
type: Class
equivalent class: Class
  intersection of: membrane
  intersection of: Restriction
    on property: part of
    some values from: membrane-bounded organelle
subclass of: membrane
subclass of: Restriction
  on property: part of
  some values from: membrane-bounded organelle

regulation of cellular metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular metabolic process
subclass of: regulation of metabolic process
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cellular metabolic process

negative regulation of cellular metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cellular metabolic process
subclass of: negative regulation of metabolic process
subclass of: regulation of cellular metabolic process
subclass of: negative regulation of cellular process
subclass of: Restriction
  on property: negatively regulates
  some values from: cellular metabolic process

positive regulation of cellular metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cellular metabolic process
subclass of: positive regulation of metabolic process
subclass of: regulation of cellular metabolic process
subclass of: positive regulation of cellular process
subclass of: Restriction
  on property: positively regulates
  some values from: cellular metabolic process

regulation of cellular biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular biosynthetic process
subclass of: regulation of biosynthetic process
subclass of: regulation of cellular metabolic process
subclass of: Restriction
  on property: regulates
  some values from: cellular biosynthetic process

negative regulation of cellular biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cellular biosynthetic process
subclass of: negative regulation of biosynthetic process
subclass of: negative regulation of cellular metabolic process
subclass of: regulation of cellular biosynthetic process
subclass of: Restriction
  on property: negatively regulates
  some values from: cellular biosynthetic process

positive regulation of cellular biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cellular biosynthetic process
subclass of: positive regulation of biosynthetic process
subclass of: positive regulation of cellular metabolic process
subclass of: regulation of cellular biosynthetic process
subclass of: Restriction
  on property: positively regulates
  some values from: cellular biosynthetic process

regulation of nervous system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: nervous system process
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: nervous system process

negative regulation of nervous system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: nervous system process
subclass of: regulation of nervous system process
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: nervous system process

positive regulation of nervous system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: nervous system process
subclass of: regulation of nervous system process
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: nervous system process

locomotion involved in locomotory behavior
type: Class
equivalent class: Class
  intersection of: locomotion
  intersection of: Restriction
    on property: part of
    some values from: locomotory behavior
subclass of: locomotion
subclass of: Restriction
  on property: part of
  some values from: locomotory behavior

positive regulation of insulin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: insulin secretion
subclass of: positive regulation of protein secretion
subclass of: regulation of insulin secretion
subclass of: positive regulation of peptide hormone secretion
subclass of: Restriction
  on property: positively regulates
  some values from: insulin secretion

regulation of response to external stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: response to external stimulus
subclass of: regulation of response to stimulus
subclass of: Restriction
  on property: regulates
  some values from: response to external stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

negative regulation of response to external stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: response to external stimulus
subclass of: regulation of response to external stimulus
subclass of: negative regulation of response to stimulus
subclass of: Restriction
  on property: negatively regulates
  some values from: response to external stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

positive regulation of response to external stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: response to external stimulus
subclass of: regulation of response to external stimulus
subclass of: positive regulation of response to stimulus
subclass of: Restriction
  on property: positively regulates
  some values from: response to external stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

regulation of lipid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: lipid transport
subclass of: regulation of transport
subclass of: regulation of lipid localization
subclass of: Restriction
  on property: regulates
  some values from: lipid transport

negative regulation of lipid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: lipid transport
subclass of: regulation of lipid transport
subclass of: negative regulation of transport
subclass of: negative regulation of lipid localization
subclass of: Restriction
  on property: negatively regulates
  some values from: lipid transport

positive regulation of lipid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: lipid transport
subclass of: regulation of lipid transport
subclass of: positive regulation of transport
subclass of: positive regulation of lipid localization
subclass of: Restriction
  on property: positively regulates
  some values from: lipid transport

regulation of intracellular transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: intracellular transport
subclass of: regulation of transport
subclass of: regulation of cellular localization
subclass of: Restriction
  on property: regulates
  some values from: intracellular transport

negative regulation of intracellular transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: intracellular transport
subclass of: regulation of intracellular transport
subclass of: negative regulation of cellular process
subclass of: negative regulation of transport
subclass of: Restriction
  on property: negatively regulates
  some values from: intracellular transport

positive regulation of intracellular transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: intracellular transport
subclass of: regulation of intracellular transport
subclass of: positive regulation of cellular process
subclass of: positive regulation of transport
subclass of: Restriction
  on property: positively regulates
  some values from: intracellular transport

multicellular organismal process
type: Class
subclass of: biological_process
RO_0002161: NCBITaxon 2
RO_0002161: NCBITaxon 2157
RO_0002161: NCBITaxon 4896
RO_0002161: NCBITaxon 4932

developmental process
type: Class
subclass of: biological_process

multicellular organism reproduction
type: Class
subclass of: reproduction
subclass of: multicellular organismal process

protein transport within lipid bilayer
type: Class
equivalent class: Class
  intersection of: protein transport
  intersection of: Restriction
    on property: occurs in
    some values from: membrane
subclass of: intracellular protein transport
subclass of: membrane organization
subclass of: Restriction
  on property: occurs in
  some values from: membrane

monocarboxylic acid metabolic process
type: Class
subclass of: carboxylic acid metabolic process

plasma membrane bounded cell projection cytoplasm
type: Class
equivalent class: Class
  intersection of: cytoplasm
  intersection of: Restriction
    on property: part of
    some values from: plasma membrane bounded cell projection
subclass of: cytoplasmic region
subclass of: Restriction
  on property: part of
  some values from: plasma membrane bounded cell projection

regulation of localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: localization
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: localization

regulation of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: protein localization
subclass of: regulation of cellular localization
subclass of: Restriction
  on property: regulates
  some values from: protein localization
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22021

regulation of organic acid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: organic acid transport
subclass of: regulation of transport
subclass of: Restriction
  on property: regulates
  some values from: organic acid transport

negative regulation of organic acid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: organic acid transport
subclass of: regulation of organic acid transport
subclass of: negative regulation of transport
subclass of: Restriction
  on property: negatively regulates
  some values from: organic acid transport

positive regulation of organic acid transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: organic acid transport
subclass of: regulation of organic acid transport
subclass of: positive regulation of transport
subclass of: Restriction
  on property: positively regulates
  some values from: organic acid transport

secretion by cell
type: Class
subclass of: secretion
subclass of: export from cell

secretion by tissue
type: Class
subclass of: multicellular organismal process
subclass of: secretion

protein-containing complex
type: Class
subclass of: complex of molecular entities
subclass of: cellular_component
subclass of: Restriction
  on property: has part
  some values from: gene product
comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
comment: This is not covalently bonded, which conflicts with changes to the parent definition.
label: protein-containing macromolecular complex

macromolecule localization
type: Class
subclass of: localization

regulation of intracellular protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: intracellular protein transport
subclass of: regulation of intracellular transport
subclass of: regulation of protein transport
subclass of: Restriction
  on property: regulates
  some values from: intracellular protein transport

negative regulation of catecholamine secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: catecholamine secretion
subclass of: regulation of catecholamine secretion
subclass of: negative regulation of amine transport
subclass of: negative regulation of secretion by cell
subclass of: Restriction
  on property: negatively regulates
  some values from: catecholamine secretion

positive regulation of catecholamine secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: catecholamine secretion
subclass of: regulation of catecholamine secretion
subclass of: positive regulation of amine transport
subclass of: positive regulation of secretion by cell
subclass of: Restriction
  on property: positively regulates
  some values from: catecholamine secretion

negative regulation of kinase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: kinase activity
subclass of: negative regulation of phosphorylation
subclass of: regulation of kinase activity
subclass of: negative regulation of transferase activity
subclass of: Restriction
  on property: negatively regulates
  some values from: kinase activity

positive regulation of kinase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: kinase activity
subclass of: positive regulation of phosphorylation
subclass of: regulation of kinase activity
subclass of: positive regulation of transferase activity
subclass of: Restriction
  on property: positively regulates
  some values from: kinase activity

tube formation
type: Class
subclass of: anatomical structure formation involved in morphogenesis
subclass of: Restriction
  on property: part of
  some values from: tube morphogenesis

tube morphogenesis
type: Class
subclass of: anatomical structure morphogenesis
subclass of: Restriction
  on property: part of
  some values from: tube development

tube development
type: Class
subclass of: anatomical structure development
subclass of: Restriction
  on property: part of
  some values from: multicellular organism development

establishment of protein localization to extracellular region
type: Class
subclass of: establishment of protein localization
subclass of: protein localization to extracellular region

locomotion
type: Class
subclass of: biological_process
RO_0002161: NCBITaxon_451864

regulation of locomotion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: locomotion
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: locomotion

negative regulation of locomotion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: locomotion
subclass of: regulation of locomotion
subclass of: negative regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: locomotion

embryonic cleavage
type: Class
subclass of: cell division
subclass of: Restriction
  on property: part of
  some values from: embryo development

positive regulation of locomotion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: locomotion
subclass of: regulation of locomotion
subclass of: positive regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: locomotion

positive regulation of embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: embryo development
subclass of: regulation of embryonic development
subclass of: positive regulation of developmental process
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: embryo development

cell migration involved in gastrulation
type: Class
equivalent class: Class
  intersection of: cell migration
  intersection of: Restriction
    on property: part of
    some values from: gastrulation
subclass of: ameboidal-type cell migration
subclass of: Restriction
  on property: part of
  some values from: gastrulation

cellular ketone metabolic process
type: Class
subclass of: cellular metabolic process
subclass of: small molecule metabolic process
subclass of: organic substance metabolic process

response to chemical
type: Class
subclass of: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

negative regulation of circadian sleep/wake cycle, sleep
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: circadian sleep/wake cycle, sleep
subclass of: negative regulation of circadian rhythm
subclass of: regulation of circadian sleep/wake cycle, sleep
subclass of: negative regulation of behavior
subclass of: Restriction
  on property: negatively regulates
  some values from: circadian sleep/wake cycle, sleep

regulation of phosphorylation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: phosphorylation
subclass of: regulation of phosphate metabolic process
subclass of: Restriction
  on property: regulates
  some values from: phosphorylation

negative regulation of phosphorylation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: phosphorylation
subclass of: regulation of phosphorylation
subclass of: negative regulation of phosphate metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: phosphorylation

positive regulation of phosphorylation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: phosphorylation
subclass of: regulation of phosphorylation
subclass of: positive regulation of phosphate metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: phosphorylation

circadian sleep/wake cycle
type: Class
subclass of: circadian behavior

regulation of circadian sleep/wake cycle
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: circadian sleep/wake cycle
subclass of: regulation of circadian rhythm
subclass of: regulation of behavior
subclass of: Restriction
  on property: regulates
  some values from: circadian sleep/wake cycle

regulation of circadian rhythm
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: circadian rhythm
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: circadian rhythm

positive regulation of circadian rhythm
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: circadian rhythm
subclass of: regulation of circadian rhythm
subclass of: positive regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: circadian rhythm

negative regulation of circadian rhythm
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: circadian rhythm
subclass of: regulation of circadian rhythm
subclass of: negative regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: circadian rhythm

amide transport
type: Class
subclass of: nitrogen compound transport

cell projection
type: Class
subclass of: cellular anatomical entity

neuron projection
type: Class
subclass of: plasma membrane bounded cell projection
RO_0002161: NCBITaxon 4751

chordate embryonic development
type: Class
subclass of: embryo development ending in birth or egg hatching

positive regulation of catalytic activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: catalytic activity
subclass of: positive regulation of molecular function
subclass of: regulation of catalytic activity
subclass of: Restriction
  on property: positively regulates
  some values from: catalytic activity

negative regulation of catalytic activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: catalytic activity
subclass of: negative regulation of molecular function
subclass of: regulation of catalytic activity
subclass of: Restriction
  on property: negatively regulates
  some values from: catalytic activity

macromolecule metabolic process
type: Class
subclass of: organic substance metabolic process

organelle
type: Class
subclass of: cellular anatomical entity

membrane-bounded organelle
type: Class
equivalent class: Class
  intersection of: organelle
  intersection of: Restriction
    on property: has part
    some values from: membrane
subclass of: organelle
subclass of: Restriction
  on property: has part
  some values from: membrane

non-membrane-bounded organelle
type: Class
subclass of: organelle
IAO_0000233: https://github.com/geneontology/go-ontology/issues/21881

intracellular organelle
type: Class
equivalent class: Class
  intersection of: organelle
  intersection of: Restriction
    on property: part of
    some values from: intracellular anatomical structure
subclass of: organelle
subclass of: Restriction
  on property: part of
  some values from: intracellular anatomical structure

intracellular membrane-bounded organelle
type: Class
equivalent class: Class
  intersection of: membrane-bounded organelle
  intersection of: Restriction
    on property: part of
    some values from: intracellular anatomical structure
subclass of: membrane-bounded organelle
subclass of: intracellular organelle

intracellular non-membrane-bounded organelle
type: Class
equivalent class: Class
  intersection of: non-membrane-bounded organelle
  intersection of: Restriction
    on property: part of
    some values from: intracellular anatomical structure
subclass of: non-membrane-bounded organelle
subclass of: intracellular organelle

regulation of monoatomic ion transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: monoatomic ion transport
subclass of: regulation of transport
subclass of: Restriction
  on property: regulates
  some values from: monoatomic ion transport

positive regulation of monoatomic ion transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: monoatomic ion transport
subclass of: regulation of monoatomic ion transport
subclass of: positive regulation of transport
subclass of: Restriction
  on property: positively regulates
  some values from: monoatomic ion transport

negative regulation of monoatomic ion transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: monoatomic ion transport
subclass of: regulation of monoatomic ion transport
subclass of: negative regulation of transport
subclass of: Restriction
  on property: negatively regulates
  some values from: monoatomic ion transport

oxoacid metabolic process
type: Class
subclass of: organic acid metabolic process

regulation of generation of precursor metabolites and energy
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: generation of precursor metabolites and energy
subclass of: regulation of cellular metabolic process
subclass of: Restriction
  on property: regulates
  some values from: generation of precursor metabolites and energy

regulation of carbohydrate catabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: carbohydrate catabolic process
subclass of: regulation of carbohydrate metabolic process
subclass of: regulation of catabolic process
subclass of: Restriction
  on property: regulates
  some values from: carbohydrate catabolic process

regulation of kinase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: kinase activity
subclass of: regulation of phosphorylation
subclass of: regulation of transferase activity
subclass of: Restriction
  on property: regulates
  some values from: kinase activity

regulation of respiratory gaseous exchange
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: respiratory gaseous exchange by respiratory system
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: regulates
  some values from: respiratory gaseous exchange by respiratory system

regulation of system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: system process
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: regulates
  some values from: system process

regulation of digestive system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: digestive system process
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: digestive system process

regulation of endocrine process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: endocrine process
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: endocrine process

regulation of respiratory system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: respiratory system process
subclass of: regulation of respiratory gaseous exchange
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: respiratory system process

negative regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: molecular_function
subclass of: regulation of molecular function
subclass of: Restriction
  on property: negatively regulates
  some values from: molecular_function

positive regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: molecular_function
subclass of: regulation of molecular function
subclass of: Restriction
  on property: positively regulates
  some values from: molecular_function

cellular metabolic process
type: Class
subclass of: metabolic process
subclass of: cellular process
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.

primary metabolic process
type: Class
subclass of: metabolic process

cellular biosynthetic process
type: Class
subclass of: biosynthetic process
subclass of: cellular metabolic process

small molecule metabolic process
type: Class
subclass of: metabolic process
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.

small molecule biosynthetic process
type: Class
subclass of: biosynthetic process
subclass of: small molecule metabolic process
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.

establishment of protein localization
type: Class
subclass of: protein localization
subclass of: establishment of localization

regulation of circadian sleep/wake cycle, sleep
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: circadian sleep/wake cycle, sleep
subclass of: regulation of circadian sleep/wake cycle
subclass of: Restriction
  on property: regulates
  some values from: circadian sleep/wake cycle, sleep

negative regulation of lipid metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: lipid metabolic process
subclass of: negative regulation of metabolic process
subclass of: regulation of lipid metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: lipid metabolic process

positive regulation of lipid metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: lipid metabolic process
subclass of: positive regulation of metabolic process
subclass of: regulation of lipid metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: lipid metabolic process

negative regulation of carbohydrate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: carbohydrate metabolic process
subclass of: regulation of carbohydrate metabolic process
subclass of: negative regulation of metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: carbohydrate metabolic process

positive regulation of carbohydrate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: carbohydrate metabolic process
subclass of: regulation of carbohydrate metabolic process
subclass of: positive regulation of metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: carbohydrate metabolic process

negative regulation of muscle contraction
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: muscle contraction
subclass of: regulation of muscle contraction
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: muscle contraction

positive regulation of muscle contraction
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: muscle contraction
subclass of: regulation of muscle contraction
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: muscle contraction

negative regulation of phosphate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: phosphate-containing compound metabolic process
subclass of: negative regulation of phosphorus metabolic process
subclass of: regulation of phosphate metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: phosphate-containing compound metabolic process

positive regulation of phosphate metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: phosphate-containing compound metabolic process
subclass of: positive regulation of phosphorus metabolic process
subclass of: regulation of phosphate metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: phosphate-containing compound metabolic process

positive regulation of circadian sleep/wake cycle, sleep
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: circadian sleep/wake cycle, sleep
subclass of: positive regulation of circadian rhythm
subclass of: regulation of circadian sleep/wake cycle, sleep
subclass of: positive regulation of behavior
subclass of: Restriction
  on property: positively regulates
  some values from: circadian sleep/wake cycle, sleep

negative regulation of embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: embryo development
subclass of: regulation of embryonic development
subclass of: negative regulation of developmental process
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: embryo development

regulation of embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: embryo development
subclass of: regulation of multicellular organismal development
subclass of: Restriction
  on property: regulates
  some values from: embryo development

carboxylic acid biosynthetic process
type: Class
subclass of: organic acid biosynthetic process
subclass of: carboxylic acid metabolic process

negative regulation of insulin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: insulin secretion
subclass of: negative regulation of protein secretion
subclass of: regulation of insulin secretion
subclass of: negative regulation of peptide hormone secretion
subclass of: Restriction
  on property: negatively regulates
  some values from: insulin secretion

acid secretion
type: Class
subclass of: secretion

hormone secretion
type: Class
subclass of: hormone transport
subclass of: signal release

regulation of hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: hormone secretion
subclass of: regulation of cell communication
subclass of: regulation of hormone levels
subclass of: regulation of signaling
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: regulates
  some values from: hormone secretion

positive regulation of hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: hormone secretion
subclass of: positive regulation of cell communication
subclass of: positive regulation of signaling
subclass of: regulation of hormone secretion
subclass of: positive regulation of secretion by cell
subclass of: Restriction
  on property: positively regulates
  some values from: hormone secretion

negative regulation of hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: hormone secretion
subclass of: negative regulation of cell communication
subclass of: negative regulation of signaling
subclass of: regulation of hormone secretion
subclass of: negative regulation of secretion by cell
subclass of: Restriction
  on property: negatively regulates
  some values from: hormone secretion

positive regulation of lipid biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: lipid biosynthetic process
subclass of: positive regulation of biosynthetic process
subclass of: positive regulation of lipid metabolic process
subclass of: regulation of lipid biosynthetic process
subclass of: Restriction
  on property: positively regulates
  some values from: lipid biosynthetic process

regulation of lipid biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: lipid biosynthetic process
subclass of: regulation of biosynthetic process
subclass of: regulation of lipid metabolic process
subclass of: Restriction
  on property: regulates
  some values from: lipid biosynthetic process

secretion
type: Class
subclass of: transport

intracellular transport
type: Class
equivalent class: Class
  intersection of: transport
  intersection of: Restriction
    on property: occurs in
    some values from: intracellular anatomical structure
subclass of: transport
subclass of: cellular localization
subclass of: establishment of localization in cell
subclass of: Restriction
  on property: occurs in
  some values from: intracellular anatomical structure

carboxylic acid transport
type: Class
subclass of: organic anion transport
subclass of: organic acid transport

mesoderm morphogenesis
type: Class
subclass of: tissue morphogenesis
subclass of: Restriction
  on property: part of
  some values from: mesoderm development

rhythmic process
type: Class
subclass of: biological_process

circadian behavior
type: Class
subclass of: rhythmic behavior
subclass of: circadian rhythm

animal organ development
type: Class
subclass of: anatomical structure development

positive regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: biological_process
subclass of: regulation of biological process
subclass of: Restriction
  on property: positively regulates
  some values from: biological_process

negative regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: biological_process
subclass of: regulation of biological process
subclass of: Restriction
  on property: negatively regulates
  some values from: biological_process

positive regulation of behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: behavior
subclass of: regulation of behavior
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: behavior

negative regulation of behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: behavior
subclass of: regulation of behavior
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: behavior

positive regulation of cellular process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cellular process
subclass of: positive regulation of biological process
subclass of: regulation of cellular process
subclass of: Restriction
  on property: positively regulates
  some values from: cellular process

negative regulation of cellular process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cellular process
subclass of: negative regulation of biological process
subclass of: regulation of cellular process
subclass of: Restriction
  on property: negatively regulates
  some values from: cellular process

regulation of post-embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: post-embryonic development
subclass of: regulation of multicellular organismal development
subclass of: Restriction
  on property: regulates
  some values from: post-embryonic development

negative regulation of post-embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: post-embryonic development
subclass of: regulation of post-embryonic development
subclass of: negative regulation of developmental process
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: post-embryonic development

positive regulation of post-embryonic development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: post-embryonic development
subclass of: regulation of post-embryonic development
subclass of: positive regulation of developmental process
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: post-embryonic development

regulation of response to stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: response to stimulus
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

positive regulation of response to stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: response to stimulus
subclass of: positive regulation of biological process
subclass of: regulation of response to stimulus
subclass of: Restriction
  on property: positively regulates
  some values from: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

negative regulation of response to stimulus
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: response to stimulus
subclass of: negative regulation of biological process
subclass of: regulation of response to stimulus
subclass of: Restriction
  on property: negatively regulates
  some values from: response to stimulus
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

embryonic morphogenesis
type: Class
subclass of: anatomical structure morphogenesis
subclass of: Restriction
  on property: part of
  some values from: embryo development

multicellular organismal reproductive process
type: Class
subclass of: reproductive process
subclass of: Restriction
  on property: part of
  some values from: multicellular organism reproduction

anatomical structure formation involved in morphogenesis
type: Class
subclass of: developmental process
subclass of: Restriction
  on property: part of
  some values from: anatomical structure morphogenesis
comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.

tissue morphogenesis
type: Class
subclass of: anatomical structure morphogenesis
subclass of: Restriction
  on property: part of
  some values from: tissue development

system development
type: Class
subclass of: anatomical structure development
subclass of: Restriction
  on property: part of
  some values from: multicellular organism development

anatomical structure development
type: Class
subclass of: developmental process

cell motility
type: Class
subclass of: cellular process
IAO_0000233: https://github.com/geneontology/go-ontology/issues/19809

catecholamine secretion
type: Class
subclass of: secretion by cell
subclass of: catecholamine transport

regulation of catecholamine secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: catecholamine secretion
subclass of: regulation of amine transport
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: regulates
  some values from: catecholamine secretion

regulation of protein secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: protein secretion
subclass of: regulation of protein transport
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: regulates
  some values from: protein secretion

negative regulation of protein secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: protein secretion
subclass of: regulation of protein secretion
subclass of: negative regulation of protein transport
subclass of: negative regulation of secretion by cell
subclass of: Restriction
  on property: negatively regulates
  some values from: protein secretion

positive regulation of protein secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: protein secretion
subclass of: regulation of protein secretion
subclass of: positive regulation of protein transport
subclass of: positive regulation of secretion by cell
subclass of: Restriction
  on property: positively regulates
  some values from: protein secretion

regulation of biological process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: biological_process
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: biological_process

regulation of catalytic activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: catalytic activity
subclass of: regulation of molecular function
subclass of: Restriction
  on property: regulates
  some values from: catalytic activity

regulation of developmental process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: developmental process
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: developmental process

regulation of cellular process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular process
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: cellular process

regulation of behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: behavior
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: regulates
  some values from: behavior

regulation of insulin secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: insulin secretion
subclass of: regulation of protein secretion
subclass of: regulation of peptide hormone secretion
subclass of: Restriction
  on property: regulates
  some values from: insulin secretion

circadian sleep/wake cycle, sleep
type: Class
equivalent class: Class
  intersection of: sleep
  intersection of: Restriction
    on property: part of
    some values from: circadian sleep/wake cycle
subclass of: circadian sleep/wake cycle process
subclass of: sleep

nervous system process
type: Class
subclass of: system process
IAO_0000233: https://github.com/geneontology/go-ontology/issues/13824

regulation of body fluid levels
type: Class
subclass of: regulation of biological quality

multicellular organismal movement
type: Class
subclass of: multicellular organismal process

musculoskeletal movement
type: Class
subclass of: multicellular organismal movement
subclass of: neuromuscular process

neuromuscular process controlling balance
type: Class
subclass of: neuromuscular process
subclass of: Restriction
  on property: has part
  some values from: musculoskeletal movement

endocrine process
type: Class
subclass of: system process

cognition
type: Class
subclass of: nervous system process

response to stimulus
type: Class
subclass of: biological_process
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

neuromuscular process
type: Class
subclass of: nervous system process

detection of stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of stimulus
subclass of: Restriction
  on property: part of
  some values from: sensory perception

detection of chemical stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of chemical stimulus
subclass of: detection of stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of chemical stimulus

detection of light stimulus involved in visual perception
type: Class
equivalent class: Class
  intersection of: detection of light stimulus
  intersection of: Restriction
    on property: part of
    some values from: visual perception
subclass of: detection of visible light
subclass of: detection of light stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: visual perception

sensory perception of taste
type: Class
subclass of: sensory perception of chemical stimulus

detection of mechanical stimulus involved in sensory perception of sound
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of sound
subclass of: nervous system process
subclass of: detection of mechanical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of sound

detection of chemical stimulus involved in sensory perception of smell
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of smell
subclass of: detection of chemical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of smell

detection of chemical stimulus involved in sensory perception of taste
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of taste
subclass of: detection of chemical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of taste

sensory perception of temperature stimulus
type: Class
subclass of: sensory perception

sensory perception of light stimulus
type: Class
subclass of: sensory perception

sensory perception of mechanical stimulus
type: Class
subclass of: sensory perception

thermoception
type: Class
subclass of: sensory perception of temperature stimulus

equilibrioception
type: Class
subclass of: sensory perception
subclass of: Restriction
  on property: part of
  some values from: neuromuscular process controlling balance

detection of temperature stimulus involved in thermoception
type: Class
equivalent class: Class
  intersection of: detection of temperature stimulus
  intersection of: Restriction
    on property: part of
    some values from: thermoception
subclass of: detection of temperature stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: thermoception

detection of temperature stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of temperature stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of temperature stimulus
subclass of: detection of stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of temperature stimulus

detection of light stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of light stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of light stimulus
subclass of: detection of stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of light stimulus

detection of temperature stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of temperature stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of temperature stimulus involved in sensory perception
subclass of: detection of stimulus involved in sensory perception of pain

detection of mechanical stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of mechanical stimulus involved in sensory perception
subclass of: detection of stimulus involved in sensory perception of pain

detection of chemical stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of chemical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of chemical stimulus involved in sensory perception
subclass of: detection of stimulus involved in sensory perception of pain

detection of mechanical stimulus involved in equilibrioception
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: equilibrioception
subclass of: detection of mechanical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: equilibrioception

detection of mechanical stimulus involved in sensory perception
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception
subclass of: detection of stimulus involved in sensory perception
subclass of: detection of mechanical stimulus
subclass of: Restriction
  on property: part of
  some values from: sensory perception of mechanical stimulus

sensory perception of touch
type: Class
subclass of: sensory perception of mechanical stimulus

detection of mechanical stimulus involved in sensory perception of touch
type: Class
equivalent class: Class
  intersection of: detection of mechanical stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of touch
subclass of: detection of mechanical stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of touch

detection of mechanical stimulus
type: Class
subclass of: detection of external stimulus
subclass of: detection of abiotic stimulus
subclass of: response to mechanical stimulus

regulation of secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: secretion
subclass of: regulation of transport
subclass of: Restriction
  on property: regulates
  some values from: secretion

positive regulation of secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: secretion
subclass of: regulation of secretion
subclass of: positive regulation of transport
subclass of: Restriction
  on property: positively regulates
  some values from: secretion

negative regulation of secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: secretion
subclass of: regulation of secretion
subclass of: negative regulation of transport
subclass of: Restriction
  on property: negatively regulates
  some values from: secretion

regulation of transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: transport
subclass of: regulation of localization
subclass of: Restriction
  on property: regulates
  some values from: transport

positive regulation of transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: transport
subclass of: positive regulation of biological process
subclass of: regulation of transport
subclass of: Restriction
  on property: positively regulates
  some values from: transport

negative regulation of transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: transport
subclass of: negative regulation of biological process
subclass of: regulation of transport
subclass of: Restriction
  on property: negatively regulates
  some values from: transport

negative regulation of lipid biosynthetic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: lipid biosynthetic process
subclass of: negative regulation of biosynthetic process
subclass of: negative regulation of lipid metabolic process
subclass of: regulation of lipid biosynthetic process
subclass of: Restriction
  on property: negatively regulates
  some values from: lipid biosynthetic process

negative regulation of developmental process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: developmental process
subclass of: negative regulation of biological process
subclass of: regulation of developmental process
subclass of: Restriction
  on property: negatively regulates
  some values from: developmental process

positive regulation of developmental process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: developmental process
subclass of: positive regulation of biological process
subclass of: regulation of developmental process
subclass of: Restriction
  on property: positively regulates
  some values from: developmental process

regulation of cellular component organization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular component organization
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cellular component organization

negative regulation of cellular component organization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cellular component organization
subclass of: negative regulation of cellular process
subclass of: regulation of cellular component organization
subclass of: Restriction
  on property: negatively regulates
  some values from: cellular component organization

positive regulation of cellular component organization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cellular component organization
subclass of: positive regulation of cellular process
subclass of: regulation of cellular component organization
subclass of: Restriction
  on property: positively regulates
  some values from: cellular component organization

regulation of phosphorus metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: phosphorus metabolic process
subclass of: regulation of cellular metabolic process
subclass of: Restriction
  on property: regulates
  some values from: phosphorus metabolic process

localization
type: Class
subclass of: biological_process

positive regulation of protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: protein transport
subclass of: positive regulation of transport
subclass of: regulation of protein transport
subclass of: positive regulation of establishment of protein localization
subclass of: Restriction
  on property: positively regulates
  some values from: protein transport

regulation of protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: protein transport
subclass of: regulation of transport
subclass of: regulation of establishment of protein localization
subclass of: Restriction
  on property: regulates
  some values from: protein transport

negative regulation of protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: protein transport
subclass of: negative regulation of transport
subclass of: regulation of protein transport
subclass of: negative regulation of establishment of protein localization
subclass of: Restriction
  on property: negatively regulates
  some values from: protein transport

establishment of localization
type: Class
subclass of: localization

regulation of multicellular organismal process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: multicellular organismal process
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: multicellular organismal process

positive regulation of multicellular organismal process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: multicellular organismal process
subclass of: positive regulation of biological process
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: multicellular organismal process

negative regulation of multicellular organismal process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: multicellular organismal process
subclass of: negative regulation of biological process
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: multicellular organismal process

cell division
type: Class
subclass of: cellular process
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.

regulation of cell division
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cell division
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cell division

regulation of transferase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: transferase activity
subclass of: regulation of catalytic activity
subclass of: Restriction
  on property: regulates
  some values from: transferase activity
comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.

positive regulation of transferase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: transferase activity
subclass of: positive regulation of catalytic activity
subclass of: regulation of transferase activity
subclass of: Restriction
  on property: positively regulates
  some values from: transferase activity
comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.

negative regulation of transferase activity
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: transferase activity
subclass of: negative regulation of catalytic activity
subclass of: regulation of transferase activity
subclass of: Restriction
  on property: negatively regulates
  some values from: transferase activity
comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.

visual perception involved in equilibrioception
type: Class
equivalent class: Class
  intersection of: visual perception
  intersection of: Restriction
    on property: part of
    some values from: equilibrioception
subclass of: visual perception
subclass of: Restriction
  on property: part of
  some values from: equilibrioception

detection of stimulus
type: Class
subclass of: response to stimulus

cellular localization
type: Class
subclass of: cellular process
subclass of: localization

establishment of localization in cell
type: Class
subclass of: establishment of localization
subclass of: Restriction
  on property: part of
  some values from: cellular localization

positive regulation of cell division
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cell division
subclass of: positive regulation of cellular process
subclass of: regulation of cell division
subclass of: Restriction
  on property: positively regulates
  some values from: cell division

negative regulation of cell division
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cell division
subclass of: negative regulation of cellular process
subclass of: regulation of cell division
subclass of: Restriction
  on property: negatively regulates
  some values from: cell division

regulation of sensory perception of pain
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: sensory perception of pain
subclass of: regulation of sensory perception
subclass of: Restriction
  on property: regulates
  some values from: sensory perception of pain

regulation of sensory perception
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: sensory perception
subclass of: regulation of nervous system process
subclass of: Restriction
  on property: regulates
  some values from: sensory perception

catecholamine transport
type: Class
subclass of: monoamine transport
subclass of: organic hydroxy compound transport

regulation of amine transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: amine transport
subclass of: regulation of transport
subclass of: Restriction
  on property: regulates
  some values from: amine transport

negative regulation of amine transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: amine transport
subclass of: negative regulation of transport
subclass of: regulation of amine transport
subclass of: Restriction
  on property: negatively regulates
  some values from: amine transport

positive regulation of amine transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: amine transport
subclass of: positive regulation of transport
subclass of: regulation of amine transport
subclass of: Restriction
  on property: positively regulates
  some values from: amine transport

regulation of nervous system development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: nervous system development
subclass of: regulation of multicellular organismal development
subclass of: Restriction
  on property: regulates
  some values from: nervous system development

negative regulation of nervous system development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: nervous system development
subclass of: negative regulation of developmental process
subclass of: negative regulation of multicellular organismal process
subclass of: regulation of nervous system development
subclass of: Restriction
  on property: negatively regulates
  some values from: nervous system development

positive regulation of nervous system development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: nervous system development
subclass of: positive regulation of developmental process
subclass of: positive regulation of multicellular organismal process
subclass of: regulation of nervous system development
subclass of: Restriction
  on property: positively regulates
  some values from: nervous system development

reflex
type: Class
subclass of: response to external stimulus

vestibular reflex
type: Class
subclass of: reflex

male mating behavior
type: Class
subclass of: mating behavior

female mating behavior
type: Class
subclass of: mating behavior

regulation of macromolecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: macromolecule metabolic process
subclass of: regulation of metabolic process
subclass of: Restriction
  on property: regulates
  some values from: macromolecule metabolic process

regulation of feeding behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: feeding behavior
subclass of: regulation of behavior
subclass of: Restriction
  on property: regulates
  some values from: feeding behavior

regulation of cellular localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cellular localization
subclass of: regulation of localization
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cellular localization

epithelium development
type: Class
subclass of: tissue development

positive regulation of digestive system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: digestive system process
subclass of: regulation of digestive system process
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: digestive system process

negative regulation of digestive system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: digestive system process
subclass of: regulation of digestive system process
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: digestive system process

epithelial tube morphogenesis
type: Class
subclass of: morphogenesis of an epithelium
subclass of: tube morphogenesis

membrane organization
type: Class
subclass of: cellular component organization

regulation of small molecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: small molecule metabolic process
subclass of: regulation of metabolic process
subclass of: Restriction
  on property: regulates
  some values from: small molecule metabolic process

positive regulation of small molecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: small molecule metabolic process
subclass of: positive regulation of metabolic process
subclass of: regulation of small molecule metabolic process
subclass of: Restriction
  on property: positively regulates
  some values from: small molecule metabolic process

negative regulation of small molecule metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: small molecule metabolic process
subclass of: negative regulation of metabolic process
subclass of: regulation of small molecule metabolic process
subclass of: Restriction
  on property: negatively regulates
  some values from: small molecule metabolic process

detection of stimulus involved in sensory perception of pain
type: Class
equivalent class: Class
  intersection of: detection of stimulus
  intersection of: Restriction
    on property: part of
    some values from: sensory perception of pain
subclass of: detection of stimulus involved in sensory perception
subclass of: Restriction
  on property: part of
  some values from: sensory perception of pain

biological regulation
type: Class
subclass of: biological_process

regulation of biological quality
type: Class
subclass of: biological regulation

regulation of molecular function
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: molecular_function
subclass of: biological regulation
subclass of: Restriction
  on property: regulates
  some values from: molecular_function

regulation of establishment of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: establishment of protein localization
subclass of: regulation of protein localization
subclass of: Restriction
  on property: regulates
  some values from: establishment of protein localization

cellular macromolecule localization
type: Class
subclass of: macromolecule localization
subclass of: cellular localization

protein localization to extracellular region
type: Class
subclass of: protein localization

organic substance transport
type: Class
subclass of: transport

organic substance metabolic process
type: Class
subclass of: metabolic process

nitrogen compound transport
type: Class
subclass of: transport

cellular component organization or biogenesis
type: Class
subclass of: cellular process

cell periphery
type: Class
subclass of: cellular anatomical entity

epithelial tube formation
type: Class
subclass of: tube formation
subclass of: Restriction
  on property: part of
  some values from: epithelial tube morphogenesis
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22302

monocarboxylic acid biosynthetic process
type: Class
subclass of: monocarboxylic acid metabolic process
subclass of: carboxylic acid biosynthetic process

regulation of primary metabolic process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: primary metabolic process
subclass of: regulation of metabolic process
subclass of: Restriction
  on property: regulates
  some values from: primary metabolic process

regulation of response to stress
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: response to stress
subclass of: regulation of response to stimulus
subclass of: Restriction
  on property: regulates
  some values from: response to stress
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

regulation of peptide transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: peptide transport
subclass of: regulation of transport
subclass of: Restriction
  on property: regulates
  some values from: peptide transport

regulation of muscle system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: muscle system process
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: muscle system process

regulation of peptide hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: peptide hormone secretion
subclass of: regulation of peptide secretion
subclass of: regulation of hormone secretion
subclass of: Restriction
  on property: regulates
  some values from: peptide hormone secretion

positive regulation of peptide hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: peptide hormone secretion
subclass of: positive regulation of peptide secretion
subclass of: positive regulation of hormone secretion
subclass of: regulation of peptide hormone secretion
subclass of: Restriction
  on property: positively regulates
  some values from: peptide hormone secretion

negative regulation of peptide hormone secretion
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: peptide hormone secretion
subclass of: negative regulation of peptide secretion
subclass of: negative regulation of hormone secretion
subclass of: regulation of peptide hormone secretion
subclass of: Restriction
  on property: negatively regulates
  some values from: peptide hormone secretion

positive regulation of intracellular protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: intracellular protein transport
subclass of: positive regulation of intracellular transport
subclass of: regulation of intracellular protein transport
subclass of: positive regulation of protein transport
subclass of: Restriction
  on property: positively regulates
  some values from: intracellular protein transport

negative regulation of intracellular protein transport
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: intracellular protein transport
subclass of: negative regulation of intracellular transport
subclass of: regulation of intracellular protein transport
subclass of: negative regulation of protein transport
subclass of: Restriction
  on property: negatively regulates
  some values from: intracellular protein transport

regulation of locomotion involved in locomotory behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: locomotion involved in locomotory behavior
subclass of: regulation of locomotion
subclass of: regulation of behavior
subclass of: Restriction
  on property: regulates
  some values from: locomotion involved in locomotory behavior

positive regulation of locomotion involved in locomotory behavior
type: Class
equivalent class: Class
  intersection of: regulation of biological process
  intersection of: Restriction
    on property: positively regulates
    some values from: locomotion involved in locomotory behavior
subclass of: positive regulation of locomotion
subclass of: positive regulation of behavior
subclass of: regulation of locomotion involved in locomotory behavior
subclass of: Restriction
  on property: positively regulates
  some values from: locomotion involved in locomotory behavior

negative regulation of locomotion involved in locomotory behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: locomotion involved in locomotory behavior
subclass of: negative regulation of locomotion
subclass of: negative regulation of behavior
subclass of: regulation of locomotion involved in locomotory behavior
subclass of: Restriction
  on property: negatively regulates
  some values from: locomotion involved in locomotory behavior

plasma membrane region
type: Class
equivalent class: Class
  intersection of: membrane
  intersection of: Restriction
    on property: part of
    some values from: plasma membrane
subclass of: membrane
subclass of: Restriction
  on property: part of
  some values from: plasma membrane
comment: Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.

membrane protein complex
type: Class
equivalent class: Class
  intersection of: protein-containing complex
  intersection of: Restriction
    on property: part of
    some values from: membrane
subclass of: protein-containing complex
subclass of: Restriction
  on property: part of
  some values from: membrane

plasma membrane protein complex
type: Class
equivalent class: Class
  intersection of: protein-containing complex
  intersection of: Restriction
    on property: part of
    some values from: plasma membrane
subclass of: membrane protein complex
subclass of: Restriction
  on property: part of
  some values from: plasma membrane

regulation of renal system process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: renal system process
subclass of: regulation of system process
subclass of: Restriction
  on property: regulates
  some values from: renal system process

cytoplasmic region
type: Class
equivalent class: Class
  intersection of: cytoplasm
  intersection of: Restriction
    on property: part of
    some values from: cytoplasm
subclass of: cytoplasm
subclass of: Restriction
  on property: part of
  some values from: cytoplasm

cell cortex region
type: Class
equivalent class: Class
  intersection of: cell cortex
  intersection of: Restriction
    on property: part of
    some values from: cell cortex
subclass of: cell cortex
subclass of: cytoplasmic region
subclass of: Restriction
  on property: part of
  some values from: cell cortex

cellular anatomical entity
type: Class
subclass of: cellular_component

plasma membrane bounded cell projection
type: Class
equivalent class: Class
  intersection of: cell projection
  intersection of: Restriction
    on property: has part
    some values from: plasma membrane region
subclass of: cell projection
subclass of: Restriction
  on property: has part
  some values from: plasma membrane region
IAO_0000233: https://github.com/geneontology/go-ontology/issues/13193

neuron projection cytoplasm
type: Class
equivalent class: Class
  intersection of: cytoplasm
  intersection of: Restriction
    on property: part of
    some values from: neuron projection
subclass of: plasma membrane bounded cell projection cytoplasm
subclass of: Restriction
  on property: part of
  some values from: neuron projection
IAO_0000233: https://github.com/geneontology/go-ontology/issues/14472

export from cell
type: Class
subclass of: transport
subclass of: cellular process

organic substance catabolic process
type: Class
subclass of: catabolic process
subclass of: organic substance metabolic process

organic substance biosynthetic process
type: Class
subclass of: biosynthetic process
subclass of: organic substance metabolic process

response to oxygen-containing compound
type: Class
subclass of: response to chemical

regulation of male mating behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: male mating behavior
subclass of: regulation of behavior
subclass of: regulation of reproductive process
subclass of: Restriction
  on property: regulates
  some values from: male mating behavior

negative regulation of male mating behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: male mating behavior
subclass of: negative regulation of behavior
subclass of: regulation of male mating behavior
subclass of: negative regulation of reproductive process
subclass of: Restriction
  on property: negatively regulates
  some values from: male mating behavior

positive regulation of male mating behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: male mating behavior
subclass of: positive regulation of behavior
subclass of: regulation of male mating behavior
subclass of: positive regulation of reproductive process
subclass of: Restriction
  on property: positively regulates
  some values from: male mating behavior

regulation of secretion by cell
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: secretion by cell
subclass of: regulation of cellular process
subclass of: regulation of secretion
subclass of: Restriction
  on property: regulates
  some values from: secretion by cell

negative regulation of secretion by cell
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: secretion by cell
subclass of: negative regulation of cellular process
subclass of: negative regulation of secretion
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: negatively regulates
  some values from: secretion by cell

positive regulation of secretion by cell
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: secretion by cell
subclass of: positive regulation of cellular process
subclass of: positive regulation of secretion
subclass of: regulation of secretion by cell
subclass of: Restriction
  on property: positively regulates
  some values from: secretion by cell

negative regulation of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: protein localization
subclass of: regulation of protein localization
subclass of: negative regulation of cellular process
subclass of: Restriction
  on property: negatively regulates
  some values from: protein localization
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22021

positive regulation of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: protein localization
subclass of: regulation of protein localization
subclass of: positive regulation of cellular process
subclass of: Restriction
  on property: positively regulates
  some values from: protein localization
IAO_0000233: https://github.com/geneontology/go-ontology/issues/22021

negative regulation of respiratory gaseous exchange
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: respiratory gaseous exchange by respiratory system
subclass of: regulation of respiratory gaseous exchange
subclass of: negative regulation of multicellular organismal process
subclass of: Restriction
  on property: negatively regulates
  some values from: respiratory gaseous exchange by respiratory system

positive regulation of respiratory gaseous exchange
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: respiratory gaseous exchange by respiratory system
subclass of: regulation of respiratory gaseous exchange
subclass of: positive regulation of multicellular organismal process
subclass of: Restriction
  on property: positively regulates
  some values from: respiratory gaseous exchange by respiratory system

negative regulation of sensory perception of pain
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: sensory perception of pain
subclass of: negative regulation of nervous system process
subclass of: regulation of sensory perception of pain
subclass of: Restriction
  on property: negatively regulates
  some values from: sensory perception of pain

positive regulation of sensory perception of pain
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: sensory perception of pain
subclass of: positive regulation of nervous system process
subclass of: regulation of sensory perception of pain
subclass of: Restriction
  on property: positively regulates
  some values from: sensory perception of pain

negative regulation of establishment of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: establishment of protein localization
subclass of: regulation of establishment of protein localization
subclass of: negative regulation of protein localization
subclass of: Restriction
  on property: negatively regulates
  some values from: establishment of protein localization

positive regulation of establishment of protein localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: establishment of protein localization
subclass of: regulation of establishment of protein localization
subclass of: positive regulation of protein localization
subclass of: Restriction
  on property: positively regulates
  some values from: establishment of protein localization

regulation of epithelial tube formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: epithelial tube formation
subclass of: regulation of morphogenesis of an epithelium
subclass of: regulation of multicellular organismal development
subclass of: Restriction
  on property: regulates
  some values from: epithelial tube formation
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

negative regulation of epithelial tube formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: epithelial tube formation
subclass of: negative regulation of multicellular organismal process
subclass of: regulation of epithelial tube formation
subclass of: negative regulation of morphogenesis of an epithelium
subclass of: Restriction
  on property: negatively regulates
  some values from: epithelial tube formation
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

positive regulation of epithelial tube formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: epithelial tube formation
subclass of: positive regulation of multicellular organismal process
subclass of: regulation of epithelial tube formation
subclass of: positive regulation of morphogenesis of an epithelium
subclass of: Restriction
  on property: positively regulates
  some values from: epithelial tube formation
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

regulation of morphogenesis of an epithelium
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: morphogenesis of an epithelium
subclass of: regulation of anatomical structure morphogenesis
subclass of: Restriction
  on property: regulates
  some values from: morphogenesis of an epithelium
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

negative regulation of morphogenesis of an epithelium
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: morphogenesis of an epithelium
subclass of: negative regulation of developmental process
subclass of: regulation of morphogenesis of an epithelium
subclass of: Restriction
  on property: negatively regulates
  some values from: morphogenesis of an epithelium
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

positive regulation of morphogenesis of an epithelium
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: morphogenesis of an epithelium
subclass of: positive regulation of developmental process
subclass of: regulation of morphogenesis of an epithelium
subclass of: Restriction
  on property: positively regulates
  some values from: morphogenesis of an epithelium
comment: An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).

regulation of detection of mechanical stimulus involved in sensory perception of touch
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: detection of mechanical stimulus involved in sensory perception of touch
subclass of: regulation of response to external stimulus
subclass of: regulation of sensory perception
subclass of: Restriction
  on property: regulates
  some values from: detection of mechanical stimulus involved in sensory perception of touch

negative regulation of detection of mechanical stimulus involved in sensory perception of touch
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: detection of mechanical stimulus involved in sensory perception of touch
subclass of: negative regulation of nervous system process
subclass of: negative regulation of response to external stimulus
subclass of: regulation of detection of mechanical stimulus involved in sensory perception of touch
subclass of: Restriction
  on property: negatively regulates
  some values from: detection of mechanical stimulus involved in sensory perception of touch

positive regulation of detection of mechanical stimulus involved in sensory perception of touch
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: detection of mechanical stimulus involved in sensory perception of touch
subclass of: positive regulation of nervous system process
subclass of: positive regulation of response to external stimulus
subclass of: regulation of detection of mechanical stimulus involved in sensory perception of touch
subclass of: Restriction
  on property: positively regulates
  some values from: detection of mechanical stimulus involved in sensory perception of touch

regulation of mechanosensory behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: mechanosensory behavior
subclass of: regulation of response to external stimulus
subclass of: regulation of behavior
subclass of: Restriction
  on property: regulates
  some values from: mechanosensory behavior

negative regulation of mechanosensory behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: mechanosensory behavior
subclass of: negative regulation of response to external stimulus
subclass of: negative regulation of behavior
subclass of: regulation of mechanosensory behavior
subclass of: Restriction
  on property: negatively regulates
  some values from: mechanosensory behavior

positive regulation of mechanosensory behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: mechanosensory behavior
subclass of: positive regulation of response to external stimulus
subclass of: positive regulation of behavior
subclass of: regulation of mechanosensory behavior
subclass of: Restriction
  on property: positively regulates
  some values from: mechanosensory behavior

regulation of mesoderm formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: mesoderm formation
subclass of: regulation of developmental process
subclass of: Restriction
  on property: regulates
  some values from: mesoderm formation

negative regulation of mesoderm formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: mesoderm formation
subclass of: regulation of mesoderm formation
subclass of: negative regulation of mesoderm development
subclass of: Restriction
  on property: negatively regulates
  some values from: mesoderm formation

positive regulation of mesoderm formation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: mesoderm formation
subclass of: regulation of mesoderm formation
subclass of: positive regulation of mesoderm development
subclass of: Restriction
  on property: positively regulates
  some values from: mesoderm formation

regulation of lipid localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: lipid localization
subclass of: regulation of localization
subclass of: Restriction
  on property: regulates
  some values from: lipid localization

negative regulation of lipid localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: lipid localization
subclass of: negative regulation of biological process
subclass of: regulation of lipid localization
subclass of: Restriction
  on property: negatively regulates
  some values from: lipid localization

positive regulation of lipid localization
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: lipid localization
subclass of: positive regulation of biological process
subclass of: regulation of lipid localization
subclass of: Restriction
  on property: positively regulates
  some values from: lipid localization

regulation of multicellular organismal development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: multicellular organism development
subclass of: regulation of developmental process
subclass of: regulation of multicellular organismal process
subclass of: Restriction
  on property: regulates
  some values from: multicellular organism development

regulation of cell motility
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: cell motility
subclass of: regulation of locomotion
subclass of: regulation of cellular process
subclass of: Restriction
  on property: regulates
  some values from: cell motility

negative regulation of cell motility
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: cell motility
subclass of: negative regulation of locomotion
subclass of: negative regulation of cellular process
subclass of: regulation of cell motility
subclass of: Restriction
  on property: negatively regulates
  some values from: cell motility

positive regulation of cell motility
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: cell motility
subclass of: positive regulation of locomotion
subclass of: positive regulation of cellular process
subclass of: regulation of cell motility
subclass of: Restriction
  on property: positively regulates
  some values from: cell motility

regulation of reproductive process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: reproductive process
subclass of: regulation of biological process
subclass of: Restriction
  on property: regulates
  some values from: reproductive process

negative regulation of reproductive process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: reproductive process
subclass of: negative regulation of biological process
subclass of: regulation of reproductive process
subclass of: Restriction
  on property: negatively regulates
  some values from: reproductive process

positive regulation of reproductive process
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: reproductive process
subclass of: positive regulation of biological process
subclass of: regulation of reproductive process
subclass of: Restriction
  on property: positively regulates
  some values from: reproductive process

negative regulation of feeding behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: feeding behavior
subclass of: negative regulation of behavior
subclass of: regulation of feeding behavior
subclass of: Restriction
  on property: negatively regulates
  some values from: feeding behavior

positive regulation of feeding behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: feeding behavior
subclass of: positive regulation of behavior
subclass of: regulation of feeding behavior
subclass of: Restriction
  on property: positively regulates
  some values from: feeding behavior

regulation of mesoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: mesoderm development
subclass of: regulation of developmental process
subclass of: Restriction
  on property: regulates
  some values from: mesoderm development

negative regulation of mesoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: mesoderm development
subclass of: negative regulation of developmental process
subclass of: regulation of mesoderm development
subclass of: Restriction
  on property: negatively regulates
  some values from: mesoderm development

positive regulation of mesoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: mesoderm development
subclass of: positive regulation of developmental process
subclass of: regulation of mesoderm development
subclass of: Restriction
  on property: positively regulates
  some values from: mesoderm development

regulation of ectoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: ectoderm development
subclass of: regulation of developmental process
subclass of: Restriction
  on property: regulates
  some values from: ectoderm development

negative regulation of ectoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: ectoderm development
subclass of: negative regulation of developmental process
subclass of: regulation of ectoderm development
subclass of: Restriction
  on property: negatively regulates
  some values from: ectoderm development

positive regulation of ectoderm development
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: ectoderm development
subclass of: positive regulation of developmental process
subclass of: regulation of ectoderm development
subclass of: Restriction
  on property: positively regulates
  some values from: ectoderm development

negative regulation of gastrulation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: negatively regulates
    some values from: gastrulation
subclass of: regulation of gastrulation
subclass of: negative regulation of embryonic development
subclass of: Restriction
  on property: negatively regulates
  some values from: gastrulation

positive regulation of gastrulation
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: positively regulates
    some values from: gastrulation
subclass of: regulation of gastrulation
subclass of: positive regulation of embryonic development
subclass of: Restriction
  on property: positively regulates
  some values from: gastrulation

regulation of grooming behavior
type: Class
equivalent class: Class
  intersection of: biological regulation
  intersection of: Restriction
    on property: regulates
    some values from: grooming behavior
subclass of: regulation of behavior
subclass of: Restriction
  on property: regulates
  some values from: grooming behavior

body part movement
type: Class
subclass of: kinesthetic behavior
definition: A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]
date: 2011-04-14T01:03:39Z
created by: George Gkoutos
has exact synonym: stationary movement
has OBO namespace: behavior_ontology

emotional behavior
type: Class
subclass of: behavior process
definition: Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences.
date: 2011-04-14T01:03:39Z
created by: George Gkoutos
has exact synonym: affective behaviour
has exact synonym: mood
has OBO namespace: behavior_ontology

Axiom
annotated source: emotional behavior
annotated property: definition
annotated target: Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences.
source: wikipedia:Emotions

social behavior
type: Class
subclass of: behavior process
definition: "A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior]
date: 2011-04-14T01:03:39Z
created by: George Gkoutos
has exact synonym: social behaviour
has OBO namespace: behavior_ontology
xref: GO:0035176

head movement
type: Class
subclass of: body part movement
definition: A change in place or position of the portion of the organism containing the brain, mouth and main sense organs [NBO:SMAC]
date: 2011-04-14T01:03:39Z
created by: George Gkoutos
has exact synonym: move head
has OBO namespace: behavior_ontology

antipredation behavior
type: Class
subclass of: protective behavior
definition: Behavior related to defence against predation or predators.
date: 2011-04-14T01:20:02Z
created by: George Gkoutos
has exact synonym: antipredator behavior
has OBO namespace: behavior_ontology

Axiom
annotated source: antipredation behavior
annotated property: definition
annotated target: Behavior related to defence against predation or predators.
source: NBO:GVG

agonistic behavior
type: Class
subclass of: emotional behavior
subclass of: social behavior
date: 2011-03-31T11:42:15Z
created by: George Gkoutos
has exact synonym: agonism
has OBO namespace: behavior_ontology

motivation behavior
type: Class
subclass of: behavior process
definition: Behavior related to the tendency of an organism to maintain internal equilibrium.
date: 2011-04-04T08:29:40Z
created by: George Gkoutos
has alternative id: NBO:0000050
has exact synonym: behavioral homeostasis
has exact synonym: maintenance behaviour
has exact synonym: perception of need
has OBO namespace: behavior_ontology

Axiom
annotated source: motivation behavior
annotated property: definition
annotated target: Behavior related to the tendency of an organism to maintain internal equilibrium.
source: NBO:GVG

behavior process
type: Class
subclass of: behavior
definition: "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
date: 2011-04-05T09:53:10Z
created by: George Gkoutos
has alternative id: NBO:0000000
has exact synonym: behavior
has exact synonym: behaviour
has OBO namespace: behavior_ontology
xref: GO:0007610

kinesthetic behavior
type: Class
subclass of: behavior process
definition: "Movement behavior of the body or its parts."
date: 2011-04-05T02:08:47Z
created by: George Gkoutos
has OBO namespace: behavior_ontology

avoidance behavior
type: Class
subclass of: motivation behavior
definition: "Behavior related to the activity seen in animals exposed to adverse stimuli, in which the tendency to act defensively is stronger than the tendency to attack." [web:http\://www.britannica.com/EBchecked/topic/45916/avoidance-behavior]
date: 2011-04-19T03:36:00Z
created by: George Gkoutos
has OBO namespace: behavior_ontology

protective behavior
type: Class
subclass of: avoidance behavior
definition: Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively.
date: 2011-04-19T03:49:55Z
created by: George Gkoutos
has exact synonym: defense
has exact synonym: defensive behaviour
has OBO namespace: behavior_ontology

Axiom
annotated source: protective behavior
annotated property: definition
annotated target: Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively.
source: NBO:SD

regulation of behavior
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: behavior process
subclass of: behavior process
subclass of: Restriction
  on property: regulates
  some values from: behavior process
definition: "Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795]
created by: George Gkoutos
xref: GO:0050795

escape behavior
type: Class
subclass of: antipredation behavior
subclass of: agonistic behavior
definition: A behavior in which action is rapidly taken by an organism in response to possible predation, examples of which include camouflage, freezing behavior, and fleeing. [Wikipedia:Escape_response]
created by: https://orcid.org/0000-0002-9611-1279
has exact synonym: escape reaction
has exact synonym: escape response

visually guided collision avoidance behavior
type: Class
subclass of: avoidance behavior
definition: A behavior involving avoidance of or escape from approaching visual stimuli, threats, or objects which are on a collision course. [PMID:23364572]
created by: https://orcid.org/0000-0002-9611-1279

root
type: Class

Muridae
type: Class
subclass of: Muroidea
has rank: NCBITaxon family

Xenoturbellida
type: Class
subclass of: Xenacoelomorpha
has rank: NCBITaxon subphylum

Xenoturbella
type: Class
subclass of: Xenoturbellidae
has rank: NCBITaxon genus

Teleostomi
type: Class
subclass of: Gnathostomata <vertebrates>
has rank: NCBITaxon clade

Euteleostomi
type: Class
subclass of: Teleostomi
has rank: NCBITaxon clade

Ecdysozoa
type: Class
subclass of: Protostomia
has rank: NCBITaxon clade

Xenacoelomorpha
type: Class
subclass of: Bilateria
has rank: NCBITaxon phylum

cellular organisms
type: Class
subclass of: root

Dipnotetrapodomorpha
type: Class
subclass of: Sarcopterygii
has rank: NCBITaxon clade

Boreoeutheria
type: Class
subclass of: Eutheria
has rank: NCBITaxon clade

Acoelomorpha
type: Class
subclass of: Xenacoelomorpha
has rank: NCBITaxon subphylum

Osteoglossocephalai
type: Class
subclass of: Teleostei
has rank: NCBITaxon clade

Xenoturbellidae
type: Class
subclass of: Xenoturbellida
has rank: NCBITaxon family

Actinopteri
type: Class
subclass of: Actinopterygii
has rank: NCBITaxon class

Clupeocephala
type: Class
subclass of: Osteoglossocephalai

Otophysi
type: Class
subclass of: Ostariophysi
has rank: NCBITaxon clade

Cypriniphysae
type: Class
subclass of: Otophysi
has rank: NCBITaxon superorder

Otomorpha
type: Class
subclass of: Clupeocephala
has rank: NCBITaxon cohort

Myomorpha
type: Class
subclass of: Rodentia
has rank: NCBITaxon suborder

Pancrustacea
type: Class
subclass of: Mandibulata
has rank: NCBITaxon clade

Mandibulata
type: Class
subclass of: Arthropoda
has rank: NCBITaxon clade

Homininae
type: Class
subclass of: Hominidae
has rank: NCBITaxon subfamily

Danionidae
type: Class
subclass of: Cyprinoidei
has rank: NCBITaxon family

Danioninae
type: Class
subclass of: Danionidae
has rank: NCBITaxon subfamily

Eukaryota
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom

Cyprinoidei
type: Class
subclass of: Cypriniformes
has rank: NCBITaxon suborder

Euarchontoglires
type: Class
subclass of: Boreoeutheria
has rank: NCBITaxon superorder

Glires
type: Class
subclass of: Euarchontoglires
has rank: NCBITaxon clade

Simiiformes
type: Class
subclass of: Haplorrhini
has rank: NCBITaxon infraorder

Hominoidea
type: Class
subclass of: Catarrhini
has rank: NCBITaxon superfamily

Sophophora
type: Class
subclass of: Drosophila <flies,genus>
has rank: NCBITaxon subgenus

melanogaster group
type: Class
subclass of: Sophophora
has rank: species group

melanogaster subgroup
type: Class
subclass of: melanogaster group
has rank: species subgroup

Teleostei
type: Class
subclass of: Neopterygii
has rank: NCBITaxon infraclass

Ostariophysi
type: Class
subclass of: Otomorpha
has rank: NCBITaxon subcohort

Tetrapoda
type: Class
subclass of: Dipnotetrapodomorpha
has rank: NCBITaxon clade

Amniota
type: Class
subclass of: Tetrapoda
has rank: NCBITaxon clade

Theria <mammals>
type: Class
subclass of: Mammalia
has rank: NCBITaxon clade

Opisthokonta
type: Class
subclass of: Eukaryota
has rank: NCBITaxon clade

Metazoa
type: Class
subclass of: Opisthokonta
has rank: NCBITaxon kingdom

Bilateria
type: Class
subclass of: Eumetazoa
has rank: NCBITaxon clade

Protostomia
type: Class
subclass of: Bilateria
has rank: NCBITaxon clade

Neoptera
type: Class
subclass of: Pterygota <insects>
has rank: NCBITaxon infraclass

Endopterygota
type: Class
subclass of: Neoptera
has rank: NCBITaxon cohort

Deuterostomia
type: Class
subclass of: Bilateria
has rank: NCBITaxon clade

Muroidea
type: Class
subclass of: Myomorpha
has rank: NCBITaxon clade

Haplorrhini
type: Class
subclass of: Primates
has rank: NCBITaxon suborder

Murinae
type: Class
subclass of: Muridae
has rank: NCBITaxon subfamily

Mammalia
type: Class
subclass of: Amniota
has rank: NCBITaxon class

Neopterygii
type: Class
subclass of: Actinopteri
has rank: NCBITaxon subclass

Muscomorpha
type: Class
subclass of: Brachycera
has rank: NCBITaxon infraorder

Schizophora
type: Class
subclass of: Cyclorrhapha

Acalyptratae
type: Class
subclass of: Schizophora

Ephydroidea
type: Class
subclass of: Acalyptratae
has rank: NCBITaxon superfamily

Drosophilinae
type: Class
subclass of: Drosophilidae
has rank: NCBITaxon subfamily

Drosophilini
type: Class
subclass of: Drosophilinae
has rank: NCBITaxon tribe

Cyclorrhapha
type: Class
subclass of: Eremoneura
has rank: NCBITaxon clade

Eremoneura
type: Class
subclass of: Muscomorpha
has rank: NCBITaxon clade

Insecta
type: Class
subclass of: Hexapoda
has rank: NCBITaxon class

Porifera
type: Class
subclass of: Metazoa
has rank: NCBITaxon phylum

Eumetazoa
type: Class
subclass of: Metazoa
has rank: NCBITaxon clade

Arthropoda
type: Class
subclass of: Panarthropoda
has rank: NCBITaxon phylum

Hexapoda
type: Class
subclass of: Pancrustacea
has rank: NCBITaxon subphylum

Diptera
type: Class
subclass of: Endopterygota
has rank: NCBITaxon order

Brachycera
type: Class
subclass of: Diptera
has rank: NCBITaxon suborder

Drosophilidae
type: Class
subclass of: Ephydroidea
has rank: NCBITaxon family

Drosophila <flies,genus>
type: Class
subclass of: Drosophilini
has rank: NCBITaxon genus

Drosophila melanogaster
type: Class
subclass of: melanogaster subgroup
has rank: NCBITaxon species

Pterygota <insects>
type: Class
subclass of: Dicondylia
has rank: NCBITaxon subclass

Chordata
type: Class
subclass of: Deuterostomia
has rank: NCBITaxon phylum

Vertebrata <vertebrates>
type: Class
subclass of: Craniata <chordates>
has rank: NCBITaxon clade

Gnathostomata <vertebrates>
type: Class
subclass of: Vertebrata <vertebrates>
has rank: NCBITaxon clade

Actinopterygii
type: Class
subclass of: Euteleostomi
has rank: NCBITaxon superclass

Cypriniformes
type: Class
subclass of: Cypriniphysae
has rank: NCBITaxon order

Danio
type: Class
subclass of: Danioninae
has rank: NCBITaxon genus

Danio rerio
type: Class
subclass of: Danio
has rank: NCBITaxon species

Sarcopterygii
type: Class
subclass of: Euteleostomi
has rank: NCBITaxon superclass

Dicondylia
type: Class
subclass of: Insecta
has rank: NCBITaxon clade

Panarthropoda
type: Class
subclass of: Ecdysozoa
has rank: NCBITaxon clade

Craniata <chordates>
type: Class
subclass of: Chordata
has rank: NCBITaxon subphylum

Eutheria
type: Class
subclass of: Theria <mammals>
has rank: NCBITaxon clade

Primates
type: Class
subclass of: Euarchontoglires
has rank: NCBITaxon order

Catarrhini
type: Class
subclass of: Simiiformes
has rank: NCBITaxon parvorder

Hominidae
type: Class
subclass of: Hominoidea
has rank: NCBITaxon family

Homo
type: Class
subclass of: Homininae
has rank: NCBITaxon genus

Homo sapiens
type: Class
subclass of: Homo
has rank: NCBITaxon species

Rodentia
type: Class
subclass of: Glires
has rank: NCBITaxon order

quality
type: Class
subclass of: Restriction
  on property:
    inverse of: has characteristic
  some values from: Thing
subclass of: Restriction
  on property: has part
  all values from: quality
label: characteristic

Axiom
annotated source: quality
annotated property: subClassOf
annotated target: Restriction
  on property:
    inverse of: has characteristic
  some values from: Thing
comment: We should name the inverse in COB and avoid the confusing inverse(..) construct

morphology
type: Class
subclass of: physical object quality

shape
type: Class
subclass of: morphology
comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.

qualitative
type: Class
subclass of: quality
comment: TODO: define this or obsolete it and move children somewhere else.

deviation (from_normal)
type: Class
subclass of: qualitative

mass
type: Class
subclass of: physical quality
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.

structure
type: Class
subclass of: morphology

circular
type: Class
subclass of: elliptic

normal
type: Class
subclass of: qualitative
RO_0002604: PATO_0000460

elliptic
type: Class
subclass of: superelliptic

physical quality
type: Class
subclass of: physical object quality

physical object quality
type: Class
subclass of: quality
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

cylindrical
type: Class
subclass of: convex 3-D shape
subclass of: Restriction
  on property: has cross section
  some values from: circular

cellularity
type: Class
subclass of: organismal quality

multicellular
type: Class
subclass of: cellularity

organismal quality
type: Class
subclass of: physical object quality

2-D shape
type: Class
subclass of: shape

convex 3-D shape
type: Class
subclass of: 3-D shape
subclass of: Restriction
  on property: has cross section
  some values from: 2-D shape
RO_0002604: PATO_0002008
comment: Use this term or an is_a child of this term when the entire shape of the object is known.

quality of a substance
type: Class
subclass of: physical quality

3-D shape
type: Class
subclass of: shape

superelliptic
type: Class
subclass of: 2-D shape

disconnected
type: Class
subclass of: structure

system
type: Class
subclass of: material entity
definition: A material entity consisting of multiple components that are causally integrated.
IAO_0000116: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43

processual entity
type: Class
subclass of: occurrent
disjoint with: anatomical entity
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

chemosensory organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: capable of
    some values from: sensory perception of chemical stimulus
subclass of: sense organ
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: part of
  some values from: chemosensory system
subclass of: Restriction
  on property: capable of
  some values from: sensory perception of chemical stimulus

peripheral nervous system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part of
  some values from: nervous system
RO_0002175: Homo sapiens

somatic nervous system
type: Class
subclass of: organ system subdivision
subclass of: Restriction
  on property: part of
  some values from: peripheral nervous system
subclass of: Restriction
  on property: contributes to morphology of
  some values from: nervous system

sense organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: capable of
    some values from: detection of stimulus involved in sensory perception
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: sensory system
subclass of: Restriction
  on property: capable of
  some values from: detection of stimulus involved in sensory perception

anatomical structure
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: existence ends during or before
  some values from: death stage
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

organ
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: anatomical system
subclass of: Restriction
  on property: has 2D boundary
  some values from: anatomical surface
subclass of: Restriction
  on property: in taxon
  some values from: Class
    complement of: Xenoturbella
subclass of: Restriction
  on property: capable of
  some values from: biological_process
disjoint with: Restriction
  on property: in taxon
  some values from: Xenoturbella
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751
UBPROP_0000012: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4

fully formed stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: post-embryonic stage
subclass of: Restriction
  on property: preceded by
  some values from: organogenesis stage
subclass of: Restriction
  on property: precedes
  some values from: death stage

embryo stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: precedes
  some values from: fully formed stage
subclass of: Restriction
  on property: precedes
  some values from: post-embryonic stage
subclass of: Restriction
  on property: simultaneous with
  some values from: embryo development
disjoint with: post-embryonic stage

death stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: ends
  some values from: life cycle
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

post-embryonic stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: preceded by
  some values from: embryo stage
subclass of: Restriction
  on property: simultaneous with
  some values from: post-embryonic development
UBPROP_0000008: In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)

life cycle
type: Class
subclass of: processual entity
subclass of: Restriction
  on property: has part
  some values from: life cycle stage
subclass of: Restriction
  on property: ends with
  some values from: death stage
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

life cycle stage
type: Class
subclass of: processual entity
subclass of: Restriction
  on property: part of
  some values from: life cycle
IAO_0000116: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751
UBPROP_0000012: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
UBPROP_0000012: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage

zygote stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: starts
  some values from: life cycle

cleavage stage
type: Class
equivalent class: Class
  intersection of: life cycle stage
  intersection of: Restriction
    on property: simultaneous with
    some values from: embryonic cleavage
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: simultaneous with
  some values from: embryonic cleavage
subclass of: Restriction
  on property: immediately preceded by
  some values from: zygote stage

blastula stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded by
  some values from: cleavage stage
IAO_0000116: consider adding a preceding stage 'morula stage' as part of cleavage

gastrula stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded by
  some values from: blastula stage
subclass of: Restriction
  on property: simultaneous with
  some values from: gastrulation
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa

neurula stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded by
  some values from: gastrula stage
subclass of: Restriction
  on property: simultaneous with
  some values from: neural tube formation
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa

organogenesis stage
type: Class
subclass of: life cycle stage
subclass of: Restriction
  on property: part of
  some values from: embryo stage
subclass of: Restriction
  on property: preceded by
  some values from: neurula stage
subclass of: Restriction
  on property: simultaneous with
  some values from: animal organ development
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa

neuron projection bundle
type: Class
subclass of: multi cell part structure
subclass of: Restriction
  on property: part of
  some values from: nervous system
subclass of: Restriction
  on property: has part
  some values from: neuron projection

respiration organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: capable of
    some values from: respiratory gaseous exchange by respiratory system
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: respiratory system
subclass of: Restriction
  on property: capable of
  some values from: respiratory gaseous exchange by respiratory system

organism substance
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
subclass of: Restriction
  on property: has quality
  some values from: quality of a substance
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
disjoint with: immaterial anatomical entity
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

anatomical system
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: part of
  some values from: multicellular organism
subclass of: Restriction
  on property: has part
  some values from: organ
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

multicellular organism
type: Class
subclass of: multicellular anatomical structure
IAO_0000116: TODO - split body and mc organism? body continues after death stage
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751
UBPROP_0000007: organismal

anatomical cluster
type: Class
subclass of: disconnected anatomical group
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

embryo
type: Class
equivalent class: Class
  intersection of: multicellular organism
  intersection of: Restriction
    on property: existence starts with
    some values from: embryo stage
  intersection of: Restriction
    on property: existence ends with
    some values from: embryo stage
subclass of: multicellular organism
subclass of: Restriction
  on property: existence starts with
  some values from: embryo stage
subclass of: Restriction
  on property: existence ends with
  some values from: embryo stage
UBPROP_0000007: embryonic

endocrine system
type: Class
equivalent class: Class
  intersection of: non-connected functional system
  intersection of: Restriction
    on property: capable of
    some values from: endocrine process
subclass of: glandular system
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa
subclass of: Restriction
  on property: capable of
  some values from: endocrine process
subclass of: Restriction
  on property: composed primarily of
  some values from: endocrine gland
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: reproductive system
disjoint with: respiratory system
disjoint with: digestive system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: entire sense organ system
disjoint with: excretory system
UBPROP_0000007: endocrine

reproductive system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: capable of part of
    some values from: reproduction
subclass of: anatomical system
subclass of: Restriction
  on property: has part
  some values from: gonad
subclass of: Restriction
  on property: capable of part of
  some values from: reproduction
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: respiratory system
disjoint with: digestive system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: entire sense organ system
disjoint with: excretory system
IAO_0000116: consider splitting genitalia from reproductive system
UBPROP_0000202: FMA_75572

gonad
type: Class
subclass of: reproductive organ
subclass of: Restriction
  on property: contains process
  some values from: gamete generation
subclass of: Restriction
  on property: develops from
  some values from: gonad primordium
UBPROP_0000007: gonadal

respiratory system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: capable of
    some values from: respiratory gaseous exchange by respiratory system
subclass of: anatomical system
subclass of: Restriction
  on property: only in taxon
  some values from: Bilateria
subclass of: Restriction
  on property: in taxon
  some values from: Class
    complement of: Acoelomorpha
subclass of: Restriction
  on property: capable of
  some values from: respiratory system process
subclass of: Restriction
  on property: capable of
  some values from: respiratory gaseous exchange by respiratory system
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: digestive system
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: entire sense organ system
disjoint with: excretory system
disjoint with: Restriction
  on property: in taxon
  some values from: Acoelomorpha
RO_0002175: Homo sapiens

digestive system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: capable of
    some values from: digestive system process
subclass of: anatomical system
subclass of: Restriction
  on property: capable of
  some values from: digestive system process
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: nervous system
disjoint with: gustatory system
disjoint with: entire sense organ system
disjoint with: excretory system
UBPROP_0000007: digestive

nervous system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa
subclass of: Restriction
  on property: in taxon
  some values from: Class
    complement of: Porifera
subclass of: Restriction
  on property: develops from
  some values from: future nervous system
subclass of: Restriction
  on property: capable of
  some values from: nervous system process
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
subclass of: Restriction
  on property: immediate transformation of
  some values from: future nervous system
disjoint with: gustatory system
disjoint with: entire sense organ system
disjoint with: excretory system
disjoint with: Restriction
  on property: in taxon
  some values from: Porifera
RO_0002161: Porifera
UBPROP_0000007: nervous
UBPROP_0000007: neural

sensory system
type: Class
subclass of: non-connected functional system
subclass of: Restriction
  on property: part of
  some values from: entire sense organ system
subclass of: Restriction
  on property: overlaps
  some values from: nervous system
subclass of: Restriction
  on property: capable of part of
  some values from: sensory perception
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs

gustatory system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: capable of part of
    some values from: detection of chemical stimulus involved in sensory perception of taste
subclass of: anatomical system
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa
subclass of: Restriction
  on property: capable of part of
  some values from: detection of chemical stimulus involved in sensory perception of taste
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: entire sense organ system
disjoint with: excretory system
UBPROP_0000007: gustatory

primordium
type: Class
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part of
  some values from: multicellular organism

anatomical entity
type: Class
subclass of: independent continuant
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

embryonic structure
type: Class
equivalent class: Class
  intersection of: developing anatomical structure
  intersection of: Restriction
    on property: part of
    some values from: embryo
subclass of: developing anatomical structure
subclass of: Restriction
  on property: part of
  some values from: embryo

vestibulo-auditory system
type: Class
subclass of: sensory system
subclass of: Restriction
  on property: capable of part of
  some values from: sensory perception of sound

olfactory organ
type: Class
equivalent class: Class
  intersection of: sense organ
  intersection of: Restriction
    on property: capable of
    some values from: detection of chemical stimulus involved in sensory perception of smell
subclass of: sense organ
subclass of: Restriction
  on property: overlaps
  some values from: olfactory system
subclass of: Restriction
  on property: capable of
  some values from: detection of chemical stimulus involved in sensory perception of smell
IAO_0000116: An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
UBPROP_0000012: fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint

endocrine gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: endocrine system
subclass of: gland
subclass of: Restriction
  on property: part of
  some values from: endocrine system
subclass of: Restriction
  on property: capable of
  some values from: hormone secretion

gland
type: Class
subclass of: organ
subclass of: Restriction
  on property: only in taxon
  some values from: Eumetazoa
subclass of: Restriction
  on property: capable of
  some values from: secretion
subclass of: Restriction
  on property: produces
  some values from: organism substance
RO_0002171: UBERON_0001434
UBPROP_0000007: glandular

reproductive organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: capable of part of
    some values from: reproduction
subclass of: organ
subclass of: reproductive structure
subclass of: Restriction
  on property: capable of part of
  some values from: reproduction

gustatory organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: capable of part of
    some values from: detection of chemical stimulus involved in sensory perception of taste
subclass of: chemosensory organ
subclass of: Restriction
  on property: part of
  some values from: gustatory system
subclass of: Restriction
  on property: capable of part of
  some values from: detection of chemical stimulus involved in sensory perception of taste

reproductive gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: reproductive system
subclass of: gland
subclass of: reproductive structure

somatosensory system
type: Class
subclass of: sensory system
subclass of: Restriction
  on property: capable of part of
  some values from: sensory perception of pain
subclass of: Restriction
  on property: capable of part of
  some values from: sensory perception of touch

entire sense organ system
type: Class
subclass of: anatomical system
subclass of: Restriction
  on property: overlaps
  some values from: nervous system
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
disjoint with: excretory system
UBPROP_0000012: note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs

vestibular system
type: Class
equivalent class: Class
  intersection of: sensory system
  intersection of: Restriction
    on property: capable of
    some values from: equilibrioception
subclass of: sensory system
subclass of: Restriction
  on property: part of
  some values from: vestibulo-auditory system
subclass of: Restriction
  on property: capable of
  some values from: equilibrioception
subclass of: Restriction
  on property: capable of part of
  some values from: vestibular reflex

reproductive structure
type: Class
equivalent class: Class
  intersection of: multicellular anatomical structure
  intersection of: Restriction
    on property: part of
    some values from: reproductive system
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: reproductive system

multi cell part structure
type: Class
subclass of: anatomical structure
subclass of: Restriction
  on property: composed primarily of
  some values from: cellular_component

developing anatomical structure
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: capable of
  some values from: developmental process
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

gonad primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part of
  some values from: reproductive system
subclass of: Restriction
  on property: has potential to develop into
  some values from: gonad
UBPROP_0000008: this is a very broad grouping class

olfactory system
type: Class
equivalent class: Class
  intersection of: sensory system
  intersection of: Restriction
    on property: capable of
    some values from: sensory perception of smell
subclass of: chemosensory system
subclass of: Restriction
  on property: capable of
  some values from: sensory perception of smell
subclass of: Restriction
  on property: existence ends during
  some values from: fully formed stage
IAO_0000116: consider splitting into main and accessory. See also: vomeronasal organ
IAO_0000116: we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system
UBPROP_0000008: In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].

chemosensory system
type: Class
equivalent class: Class
  intersection of: sensory system
  intersection of: Restriction
    on property: capable of
    some values from: sensory perception of chemical stimulus
subclass of: sensory system
subclass of: Restriction
  on property: capable of
  some values from: sensory perception of chemical stimulus

respiratory system fluid/secretion
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: produced by
    some values from: respiratory system
subclass of: organism substance
subclass of: Restriction
  on property: produced by
  some values from: respiratory system

vestibular organ
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part of
    some values from: vestibular system
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: somatic nervous system
subclass of: Restriction
  on property: part of
  some values from: vestibular system

presumptive structure
type: Class
equivalent class: Class
  intersection of: developing anatomical structure
  intersection of: Restriction
    on property: part of
    some values from: embryo
  intersection of: Restriction
    on property: has potential to develop into
    some values from: anatomical structure
subclass of: embryonic structure
subclass of: Restriction
  on property: has potential to develop into
  some values from: anatomical structure
IAO_0000116: Consider merging with anlage

digestive system gland
type: Class
equivalent class: Class
  intersection of: endocrine gland
  intersection of: Restriction
    on property: part of
    some values from: digestive system
subclass of: endocrine gland
subclass of: digestive system element

anatomical surface
type: Class
subclass of: bona-fide anatomical boundary
comment: Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.

cleaving embryo
type: Class
equivalent class: Class
  intersection of: multicellular organism
  intersection of: Restriction
    on property: existence starts with
    some values from: cleavage stage
  intersection of: Restriction
    on property: existence ends with
    some values from: cleavage stage
subclass of: embryo
subclass of: Restriction
  on property: existence starts with
  some values from: cleavage stage
subclass of: Restriction
  on property: existence ends with
  some values from: cleavage stage

mechanosensory system
type: Class
equivalent class: Class
  intersection of: sensory system
  intersection of: Restriction
    on property: capable of
    some values from: sensory perception of mechanical stimulus
subclass of: sensory system
subclass of: Restriction
  on property: capable of
  some values from: sensory perception of mechanical stimulus

post-embryonic organism
type: Class
equivalent class: Class
  intersection of: multicellular organism
  intersection of: Restriction
    on property: existence starts with
    some values from: post-embryonic stage
subclass of: multicellular organism
subclass of: Restriction
  on property: existence starts with
  some values from: post-embryonic stage

multicellular anatomical structure
type: Class
equivalent class: Class
  intersection of: anatomical structure
  intersection of: Restriction
    on property: has quality
    some values from: multicellular
subclass of: anatomical structure
subclass of: Restriction
  on property: has quality
  some values from: multicellular
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

neuroendocrine gland
type: Class
equivalent class: Class
  intersection of: endocrine gland
  intersection of: Restriction
    on property: part of
    some values from: nervous system
subclass of: endocrine gland
subclass of: Restriction
  on property: part of
  some values from: nervous system

bona-fide anatomical boundary
type: Class
subclass of: immaterial anatomical entity
comment: One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)

organ system subdivision
type: Class
subclass of: multicellular anatomical structure
subclass of: Restriction
  on property: part of
  some values from: anatomical system
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

digestive system element
type: Class
equivalent class: Class
  intersection of: organ
  intersection of: Restriction
    on property: part of
    some values from: digestive system
subclass of: organ
subclass of: Restriction
  on property: part of
  some values from: digestive system

non-connected functional system
type: Class
subclass of: disconnected anatomical group

glandular system
type: Class
equivalent class: Class
  intersection of: non-connected functional system
  intersection of: Restriction
    on property: composed primarily of
    some values from: gland
subclass of: non-connected functional system
subclass of: Restriction
  on property: composed primarily of
  some values from: gland

auditory system
type: Class
equivalent class: Class
  intersection of: sensory system
  intersection of: Restriction
    on property: capable of
    some values from: sensory perception of sound
subclass of: mechanosensory system
subclass of: Restriction
  on property: part of
  some values from: vestibulo-auditory system
subclass of: Restriction
  on property: capable of
  some values from: sensory perception of sound

future nervous system
type: Class
equivalent class: Class
  intersection of: presumptive structure
  intersection of: Restriction
    on property: has potential to develop into
    some values from: nervous system
subclass of: presumptive structure
subclass of: Restriction
  on property: has potential to develop into
  some values from: nervous system
subclass of: Restriction
  on property: existence starts during or after
  some values from: organogenesis stage

reproductive gland secretion
type: Class
equivalent class: Class
  intersection of: organism substance
  intersection of: Restriction
    on property: produced by
    some values from: reproductive gland
subclass of: organism substance
subclass of: Restriction
  on property: produced by
  some values from: reproductive gland

disconnected anatomical group
type: Class
subclass of: material anatomical entity
subclass of: Restriction
  on property: has quality
  some values from: disconnected
subclass of: Restriction
  on property: composed primarily of
  some values from: anatomical structure
subclass of: Restriction
  on property: has component
  min qualified cardinality: 2
  on class: anatomical structure
RO_0002175: NCBITaxon_33090
RO_0002175: Metazoa
RO_0002175: NCBITaxon 4751

respiratory system gland
type: Class
equivalent class: Class
  intersection of: gland
  intersection of: Restriction
    on property: part of
    some values from: respiratory system
subclass of: gland
subclass of: Restriction
  on property: part of
  some values from: respiratory system

excretory system
type: Class
equivalent class: Class
  intersection of: anatomical system
  intersection of: Restriction
    on property: capable of
    some values from: secretion
subclass of: anatomical system
subclass of: Restriction
  on property: capable of
  some values from: secretion

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
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 regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

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

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

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

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