definition
type: AnnotationProperty

RO_0001900
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.

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.

subset_property
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

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 entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: generically dependent continuant
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

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
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
IAO_0000111: realized in
IAO_0000112: this disease is realized in this disease course
IAO_0000112: this fragility is realized in this shattering
IAO_0000112: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
domain: process
range: realizable entity
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
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
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
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.
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
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
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
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
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
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
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
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.

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
in_subset: RO_0002259
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.

derives from
type: ObjectProperty
inverse of: derives into
IAO_0000112: this cell derives from this parent cell (cell division)
IAO_0000112: this nucleus derives from this parent nucleus (nuclear division)
IAO_0000114: IAO_0000125
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
IAO_0000118: derives_from
IAO_0000232: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
in_subset: ro-eco

derives into
type: ObjectProperty
IAO_0000112: this parent cell derives into this cell (cell division)
IAO_0000112: this parent nucleus derives into this nucleus (nuclear division)
IAO_0000114: IAO_0000125
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
IAO_0000116: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
IAO_0000118: derives_into
in_subset: ro-eco

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
in_subset: ro-eco

contains
type: ObjectProperty
IAO_0000111: contains
RO_0001900: RO_0001901
in_subset: ro-eco

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
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
in_subset: valid for go gp2term

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.

bounding layer of
type: ObjectProperty
sub property of: part of
domain: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0002124
range: material entity
definition: X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.

coincident with
type: ObjectProperty
sub property of: mereotopologically related to
domain: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001199
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: PATO_0001199
definition: A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
IAO_0000116: Note from NCEAS meeting: consider changing primary label
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

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.
created by: dos
creation date: 2017-05-24T09:30:46Z

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.
created by: dos
creation date: 2017-05-24T09:31:01Z
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.
created by: dos
creation date: 2017-05-24T09:31:17Z
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
created by: dos
creation date: 2017-05-24T09:44:33Z
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.
created by: dos
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

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

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

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

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: GOC:dos

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000118: di
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
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)

during which starts
type: ObjectProperty
sub property of: temporally related to
inverse of: starts during
IAO_0000117: David Osumi-Sutherland
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
domain: occurrent
range: occurrent
IAO_0000117: David Osumi-Sutherland
IAO_0000118: io
in_subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000118: d
IAO_0000118: during
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
IAO_0000117: David Osumi-Sutherland
IAO_0000118: o
IAO_0000118: overlaps
in_subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(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
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco

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

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: David Osumi-Sutherland
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

partially overlaps
type: ObjectProperty
sub property of: overlaps
IAO_0000114: IAO_0000125
definition: x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x
IAO_0000116: We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom
IAO_0000118: proper overlaps
IAO_0000426: (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x)))))
RO_0001900: RO_0001901
in_subset: ro-eco

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: CARO_0001010
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
property chain axiom: results in developmental progression of
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: Chris Mungall
IAO_0000117: Jennifer Deegan
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/17921072
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20973947
in_subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: IAO_0000125
definition: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in_subset: ro-eco

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
property chain axiom:
  inverse of: connects
property chain axiom: connects
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

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: Restriction
  on property: part of
  some values from: system
IAO_0000112: The M8 connects Glasgow and Edinburgh
IAO_0000112: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
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
domain: CARO_0000003
range: CARO_0000003
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

drains
type: ObjectProperty
sub property of: connected to
definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
IAO_0000116: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

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
in_subset: ro-eco

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: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Melissa Haendel
IAO_0000117: Terry Meehan
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: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
in_subset: RO_0002259

directly develops from
type: ObjectProperty
sub property of: develops from
inverse of: directly develops into
domain: Class
  union of: CARO_0010000
  union of: CL_0000000
range: Class
  union of: CARO_0010000
  union of: CL_0000000
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: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: has developmental precursor
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
in_subset: RO_0002259

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: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
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
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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: Chris Mungall
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)".
in_subset: ro-eco

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: Chris Mungall
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

obsolete actively participates in
type: ObjectProperty
definition: OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role
IAO_0000117: Chris Mungall
IAO_0000118: agent in
IAO_0100001: process has causal agent
comment: Obsoleted as the inverse property was obsoleted.
deprecated: true

obsolete has active participant
type: ObjectProperty
definition: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
IAO_0000117: Chris Mungall
IAO_0000118: has agent
IAO_0100001: causal agent in process
deprecated: true

surrounded by
type: ObjectProperty
sub property of: adjacent to
inverse of: surrounds
IAO_0000114: IAO_0000125
definition: x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: IAO_0000125
definition: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

surrounds
type: ObjectProperty
sub property of: adjacent to
IAO_0000114: IAO_0000125
definition: inverse of surrounded by
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
in_subset: RO_0002259

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
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.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
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: Chris Mungall
IAO_0000119: Allen
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: started by
in_subset: ro-eco

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: Chris Mungall

develops in
type: ObjectProperty
sub property of: developmentally preceded by
domain: CARO_0000000
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: Chris Mungall
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: Chris Mungall
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: finished by
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: starts with process that occurs in
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: ends with process that occurs in
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: consumes
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: produces
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

has developmental contribution from
type: ObjectProperty
sub property of: developmentally preceded by
inverse of: developmentally contributes to
domain: CARO_0000000
range: CARO_0000000
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: Chris Mungall

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: Chris Mungall
in_subset: RO_0002259

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: Chris Mungall
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.
in_subset: valid for go gp2term

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.
has_related_synonym: affects
in_subset: valid for go gp2term

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
IAO_0000114: IAO_0000125
definition: Inverse of developmentally preceded by
IAO_0000117: Chris Mungall

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: Chris Mungall

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: CARO_0000000
IAO_0000114: IAO_0000125
definition: p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
IAO_0000116: This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
IAO_0000117: Chris Mungall

results in formation of
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
IAO_0000112: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
IAO_0000112: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
IAO_0000114: IAO_0000125
IAO_0000117: Chris Mungall
IAO_0000119: GOC:mtg_berkeley_2013
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has habitat
type: ObjectProperty
sub property of: ecologically related to
domain: CARO_0001010
range: ENVO_01000254
IAO_0000112: Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
IAO_0000114: IAO_0000428
definition: x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
IAO_0000117: Pier Buttigieg
IAO_0000118: adapted for living in
in_subset: ro-eco
comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.

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
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam
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
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam

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: Chris Mungall
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: Chris Mungall
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.

ecologically related to
type: ObjectProperty
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in_subset: ro-eco

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
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: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

contributes to
type: ObjectProperty
sub property of: capable of part of
sub property of: part of structure that is capable of
IAO_0000112: ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
IAO_0000112: Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
IAO_0000112: eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
IAO_0000116: We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
IAO_0000117: Chris Mungall
IAO_0000232: In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
in_subset: valid for go gp2term

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: Chris Mungall
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.
in_subset: valid for go gp2term

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: Chris Mungall
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: Chris Mungall
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: Chris Mungall
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: Chris Mungall
in_subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: Chris Mungall
IAO_0000589: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: Chris Mungall
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: Chris Mungall
in_subset: RO_0002259

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: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
IAO_0000117: Chris Mungall
in_subset: RO_0002259
in_subset: ro-eco

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: Chris Mungall

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: Chris Mungall
IAO_0000589: attached to (anatomical structure to anatomical structure)
in_subset: ro-eco

in branching relationship with
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: material entity
IAO_0000114: IAO_0000428
definition: A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
RO_0004036: part of

tributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River tributary_of Columbia River
IAO_0000112: inferior epigastric vein tributary_of external iliac vein
IAO_0000114: IAO_0000428
definition: x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
IAO_0000117: Chris Mungall
IAO_0000118: drains into
IAO_0000118: drains to
IAO_0000118: tributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Tributary
IAO_0000119: http://www.medindia.net/glossary/venous_tributary.htm
IAO_0000232: This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
in_subset: ro-eco

distributary of
type: ObjectProperty
sub property of: connected to
sub property of: in branching relationship with
IAO_0000112: Deschutes River distributary_of Little Lava Lake
IAO_0000114: IAO_0000428
definition: x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x
IAO_0000117: Chris Mungall
IAO_0000118: branch of
IAO_0000118: distributary channel of
IAO_0000119: http://en.wikipedia.org/wiki/Distributary
in_subset: ro-eco
comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes

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: Chris Mungall
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
domain: CARO_0000000
range: CARO_0000000
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: Chris Mungall

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: Chris Mungall

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: Chris Mungall

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: Chris Mungall

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: Chris Mungall

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: Chris Mungall

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: Chris Mungall
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: Chris Mungall
IAO_0000118: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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: Chris Mungall
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.

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

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
IAO_0000117: Chris Mungall
in_subset: valid for go annotation extension
in_subset: valid for gocam

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: Chris Mungall
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: Chris Mungall
IAO_0000118: influences (processual)
has_related_synonym: affects

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: Chris Mungall
IAO_0000119: causal-relations
in_subset: RO_0002259

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: Chris Mungall

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: Chris Mungall
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: Chris Mungall
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: Chris Mungall
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.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
IAO_0000117: Chris Mungall
IAO_0000118: executes activity in
has_exact_synonym: enables 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

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
database_cross_reference: GOC:cjm
database_cross_reference: GOC:dos

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: 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_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000117: Chris Mungall
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.
has_exact_synonym: in pairwise interaction with
in_subset: ro-eco

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: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
definition: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: Chris Mungall
IAO_0000118: interacts with on organism level
in_subset: ro-eco

trophically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
definition: An interaction relationship in which the partners are related via a feeding relationship.
IAO_0000117: Chris Mungall
in_subset: ro-eco

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
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: Chris Mungall
IAO_0000117: Vasundra Touré
has_exact_synonym: molecularly controls

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: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly inhibits
has_exact_synonym: molecularly decreases activity of

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: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly activates
has_exact_synonym: molecularly increases activity of

acquires nutrients from
type: ObjectProperty
sub property of: trophically interacts with
inverse of: provides nutrients for
IAO_0000117: Chris Mungall
IAO_0000232: Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion.
in_subset: ro-eco

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: Chris Mungall
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.

provides nutrients for
type: ObjectProperty
sub property of: trophically interacts with
IAO_0000117: Chris Mungall
in_subset: ro-eco

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: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
RO_0001900: RO_0001901
in_subset: ro-eco

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: Chris Mungall
in_subset: ro-eco

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: Chris Mungall

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: Chris Mungall

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: Chris Mungall
RO_0002575: transformation of

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: Chris Mungall
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: Chris Mungall

towards
type: ObjectProperty
sub property of: depends on
definition: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
IAO_0000116: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205

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: Chris Mungall
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.

determined by
type: ObjectProperty
sub property of: part of
sub property of: determined by part of
sub property of: causally influenced by
inverse of: determines
domain: system
range: material entity
IAO_0000112: A coral reef environment is determined by a particular coral reef
definition: s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
IAO_0000116: The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/24330602
IAO_0000589: determined by (system to material entity)
creator: Chris Mungall
creator: Pier Buttigieg
in_subset: ro-eco

determines
type: ObjectProperty
sub property of: causally influences
definition: inverse of determined by
IAO_0000117: Chris Mungall
IAO_0000589: determines (material entity to system)
in_subset: RO_0002259
in_subset: ro-eco

determined by part of
type: ObjectProperty
sub property of: overlaps
sub property of: causal relation between entities
domain: system
range: material entity
property chain axiom: determined by
property chain axiom: part of
definition: s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
IAO_0000117: Chris Mungall
in_subset: ro-eco

Axiom
annotated source: determined by part of
annotated property: propertyChainAxiom
annotated target: determined by
annotated target: part of
RO_0002582: true

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: Chris Mungall
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: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: Chris Mungall

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: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

biomechanically related to
type: ObjectProperty
sub property of: functionally related to
domain: CARO_0000003
range: CARO_0000003
definition: A relation that holds between elements of a musculoskeletal system or its analogs.
IAO_0000117: Chris Mungall
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.

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: CARO_0001010
range: CARO_0001010
IAO_0000117: Chris Mungall
in_subset: ro-eco

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: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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: Chris Mungall

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: Chris Mungall
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
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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: Melissa Haendel
in_subset: ro-eco
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: Melissa Haendel
in_subset: ro-eco

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: material entity
property chain axiom: realized in response to
property chain axiom: has input
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: cjm
creation date: 2017-12-26T19:45:49Z

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.
created by: cjm
creation date: 2018-01-25T23:20:13Z

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
created by: cjm
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

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
created by: cjm
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

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
created by: cjm
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

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
created by: cjm
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

has substance added
type: ObjectProperty
type: IrreflexiveProperty
domain: material entity
range: material entity
IAO_0000112: muffin 'has substance added' some 'baking soda'
IAO_0000114: IAO_0000428
definition: "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.
IAO_0000116: The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients.
IAO_0000117: Damion Dooley

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable entity
range: process
property chain axiom: realized in
property chain axiom: causally downstream of
IAO_0000112: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
IAO_0000112: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
IAO_0000112: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: Austin Meier
contributor: Chris Mungall
contributor: David Osumi-Sutherland
contributor: Marie Angelique Laporte
has_exact_synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: has_exact_synonym
annotated target: triggered by process
database_cross_reference: RO:cjm

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: characteristic of
property chain axiom: is concretized as
IAO_0000112: Genetic information generically depend on molecules of DNA.
IAO_0000112: The novel *War and Peace* generically depends on this copy of the novel.
IAO_0000112: The pattern shared by chess boards generically depends on any chess board.
IAO_0000112: The score of a symphony g-depends on a copy of the score.
IAO_0000112: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
IAO_0000119: [072-ISO]
has_exact_synonym: g-depends on

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: has characteristic
IAO_0000112: Molecules of DNA are carriers of genetic information.
IAO_0000112: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
IAO_0000112: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
IAO_0000119: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: Vasundra Touré

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.
created by: pg
creation date: 2022-09-26T06:07:17Z

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.
created by: pg
creation date: 2022-09-26T06:08:01Z

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
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: PATO_0000001
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.
contributor: https://orcid.org/0000-0002-8688-6599

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.
contributor: https://orcid.org/0000-0002-8688-6599

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.
contributor: https://orcid.org/0000-0002-8688-6599

continuant
type: Class
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
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.

occurrent
type: Class
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
definition: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
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.

spatial region
type: Class
subclass of: immaterial entity

process
type: Class
subclass of: occurrent
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

disposition
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: realizable entity
disjoint with: quality
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.

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
disjoint with: generically dependent continuant
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.

role
type: Class
subclass of: realizable entity
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.

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: generically dependent continuant
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

GO_0016301
type: Class
subclass of: Restriction
  on property: is kinase activity
  has self: true

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: Chris Mungall
IAO_0000119: http://www.jbiomedsem.com/content/4/1/43

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: GO_0003674
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: GO_0003674
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

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: GO_0003674
  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

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: GO_0008150
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  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