is a defining property chain axiom
type: AnnotationProperty
IAO_0000115: 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
IAO_0000115: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
IAO_0000115: 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)
IAO_0000115: 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

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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: [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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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
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)
IAO_0000115: 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

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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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)
IAO_0000115: 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
IAO_0000115: 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)
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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.

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: linear
range: Class
  intersection of: continuant
  intersection of: Restriction
    on property: has characteristic
    some values from: linear
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
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.

regulates transport of
type: ObjectProperty
property chain axiom: regulates
property chain axiom: transports or maintains localization of
IAO_0000115: A relationship that holds between a process that regulates a transport process and the entity transported by that process.
IAO_0000117: https://orcid.org/0000-0002-7073-9172
in subset: ro-eco

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
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
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
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
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:49:21Z

transports
type: ObjectProperty
sub property of: transports or maintains localization of
IAO_0000115: Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-07-20T17:11:08Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: https://orcid.org/0000-0002-7073-9172
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.
has db xref: https://orcid.org/0000-0002-7073-9172

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: IAO_0000115
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.
has db xref: https://orcid.org/0000-0002-7073-9172

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: IAO_0000115
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.
has db xref: https://orcid.org/0000-0002-7073-9172

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
IAO_0000115: 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: https://orcid.org/0000-0002-7073-9172
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: IAO_0000115
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.
has db xref: https://orcid.org/0000-0002-7073-9172

during which ends
type: ObjectProperty
sub property of: temporally related to
inverse of: ends during
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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
IAO_0000117: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: https://orcid.org/0000-0002-7073-9172
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: pending final vetting
IAO_0000115: 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

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
IAO_0000115: 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

gene product of
type: ObjectProperty
sub property of: genomically related to
inverse of: has gene product
domain: independent continuant
domain: Class
  union of: generically dependent continuant
  union of: material entity
range: continuant
range: Class
  union of: generically dependent continuant
  union of: material entity
IAO_0000114: pending final vetting
IAO_0000115: definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
IAO_0000116: We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
IAO_0000117: https://orcid.org/0000-0002-6601-2165

has gene product
type: ObjectProperty
sub property of: genomically related to
domain: continuant
range: independent continuant
IAO_0000112: every HOTAIR lncRNA is the gene product of some HOXC gene
IAO_0000112: every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
IAO_0000114: pending final vetting
IAO_0000115: x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
IAO_0000117: https://orcid.org/0000-0002-6601-2165

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
IAO_0000115: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
IAO_0000117: https://orcid.org/0000-0001-7476-6306
IAO_0000117: https://orcid.org/0000-0002-3837-8864
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
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
IAO_0000115: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
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
IAO_0000115: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
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'
IAO_0000115: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
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
IAO_0000115: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has function in

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

obsolete has active participant
type: ObjectProperty
IAO_0000115: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has agent
IAO_0100001: causal agent in process
deprecated: true

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: pending final vetting
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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.

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

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
IAO_0000114: pending final vetting
IAO_0000115: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: starts with process that occurs in
in subset: ro-eco

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
IAO_0000114: pending final vetting
IAO_0000115: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: ends with process that occurs in
in subset: ro-eco

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
IAO_0000114: pending final vetting
IAO_0000115: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: consumes
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
IAO_0000114: pending final vetting
IAO_0000115: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: produces
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

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.
IAO_0000115: 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.
IAO_0000115: 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

results in developmental progression of
type: ObjectProperty
sub property of: developmentally related to
domain: GO_0008150
range: anatomical entity
IAO_0000114: pending final vetting
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165

results in development of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: every flower development (GO:0009908) results in development of some flower (PO:0009046)
IAO_0000114: pending final vetting
IAO_0000115: p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.geneontology.org/GO.doc.development.shtml
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in formation of anatomical entity
type: ObjectProperty
sub property of: has output
sub property of: results in developmental progression of
inverse of: formed as result of
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: pending final vetting
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in morphogenesis of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
IAO_0000112: tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
IAO_0000114: pending final vetting
IAO_0000115: The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in maturation of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
IAO_0000112: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
IAO_0000112: bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
IAO_0000114: pending final vetting
IAO_0000115: The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for gocam

transports or maintains localization of
type: ObjectProperty
sub property of: related via localization to
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: regulates localization of
in subset: valid for go annotation extension
in subset: valid for go ontology
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
IAO_0000115: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

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

results in acquisition of features of
type: ObjectProperty
sub property of: results in developmental progression of
sub property of: results in changes to anatomical or cellular structure
range: anatomical structure
IAO_0000112: an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
IAO_0000115: The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: GOC:mtg_berkeley_2013
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

ecologically related to
type: ObjectProperty
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
in subset: ro-eco

mereotopologically related to
type: ObjectProperty
IAO_0000115: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
IAO_0000115: A relationship that holds between entities participating in some developmental process (GO:0032502)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
domain: material entity
range: material entity
IAO_0000112: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
IAO_0000115: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
in subset: valid for go gp2term

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: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
IAO_0000115: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
IAO_0000115: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: false

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

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
IAO_0000115: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

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
IAO_0000115: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: actively involved in
IAO_0000118: enables part of

regulates levels of
type: ObjectProperty
sub property of: functionally related to
domain: process
range: material entity
IAO_0000112: every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
IAO_0000115: p regulates levels of c if p regulates some amount (PATO:0000070) of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: regulates levels of (process to entity)

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
IAO_0000115: inverse of enables
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
IAO_0000115: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
in subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
IAO_0000115: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259

related via localization to
type: ObjectProperty
domain: process
range: continuant
IAO_0000115: A relationship that holds via some process of localization
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is a grouping relation.

has target start location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

has target end location
type: ObjectProperty
sub property of: results in transport to from or in
property chain axiom: part of
IAO_0000115: This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

imports
type: ObjectProperty
sub property of: transports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go ontology

results in transport to from or in
type: ObjectProperty
sub property of: related via localization to
IAO_0000112: 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
IAO_0000117: https://orcid.org/0000-0002-6601-2165

exports
type: ObjectProperty
sub property of: transports
IAO_0000115: Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go ontology

results in commitment to
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
IAO_0000112: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
IAO_0000115: p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

results in determination of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
IAO_0000115: p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
IAO_0000115: inverse of has input
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259
in subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
IAO_0000115: inverse of has output
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: RO_0002259
in subset: ro-eco

formed as result of
type: ObjectProperty
sub property of: output of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

results in specification of
type: ObjectProperty
sub property of: results in developmental progression of
range: cell
IAO_0000115: The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

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: requires discussion
IAO_0000115: inverse of upstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: requires discussion
IAO_0000117: https://orcid.org/0000-0002-6601-2165

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
IAO_0000115: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly activates
RO_0002579: positively regulates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
IAO_0000115: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: IAO_0000115
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.
has db xref: 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
IAO_0000115: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: has output
property chain axiom: has input
IAO_0000115: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: directly provides input for
IAO_0000119: causal-relations
IAO_0000589: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of or within, positive effect
type: TransitiveProperty
domain: process
range: process
IAO_0000114: requires discussion
IAO_0000115: transitive form of directly_provides_input_for
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.
IAO_0000589: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
property chain axiom: part of
IAO_0000115: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: influences (processual)
has related synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
IAO_0000115: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
IAO_0000115: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
IAO_0000115: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
IAO_0000112: A protein that enables activity in a cytosol.
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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: IAO_0000115
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.
has db xref: https://orcid.org/0000-0002-6601-2165
has db xref: https://orcid.org/0000-0002-7073-9172

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
IAO_0000115: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has exact synonym: in pairwise interaction with
in subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
IAO_0000115: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: binds
IAO_0000118: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
IAO_0000118: interacts with on organism level
in subset: ro-eco

symbiotically interacts with
type: ObjectProperty
sub property of: participates in a biotic-biotic interaction with
type: SymmetricProperty
IAO_0000112: whales symbiotically interact with the barnacles that attach to them
IAO_0000115: A biotic interaction in which the two organisms live together in more or less intimate association.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
in subset: ro-eco

interacts with via parasite-host interaction
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000115: An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/19278549
IAO_0000232: This relation groups a pair of inverse relations, parasite of and parasitized by
in subset: ro-eco

parasite of
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: has host
inverse of: parasitized by
IAO_0000112: Pediculus humanus capitis parasite of human
IAO_0000115: A parasite-host relationship where an organism benefits at the expense of another.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: parasitizes
has exact synonym: direct parasite of
in subset: ro-eco

parasitized by
type: ObjectProperty
sub property of: interacts with via parasite-host interaction
sub property of: host of
IAO_0000115: Inverse of parasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: has parasite
IAO_0000118: parasitised by
has exact synonym: directly parasitized by
in subset: ro-eco

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
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
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly inhibits
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
IAO_0000115: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000118: directly activates
has exact synonym: molecularly increases activity of

host of
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
in subset: ro-eco

has host
type: ObjectProperty
sub property of: symbiotically interacts with
IAO_0000115: X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
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

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

existence starts during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence starts during or after
property chain axiom: part of
IAO_0000115: x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165

existence overlaps
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
IAO_0000115: x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts and ends during
type: ObjectProperty
sub property of: existence starts during
sub property of: existence ends during
IAO_0000115: x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has exact synonym: exists during
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during
type: ObjectProperty
sub property of: existence overlaps
sub property of: existence ends during or before
property chain axiom: part of
IAO_0000115: x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence starts during or after
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: preceded by
IAO_0000115: x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

existence ends during or before
type: ObjectProperty
sub property of: relation between physical entity and a process or stage
property chain axiom: part of
property chain axiom: precedes
IAO_0000115: x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
IAO_0000115: 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
IAO_0000115: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

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

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

hyperparasite of
type: ObjectProperty
sub property of: has host
inverse of: hyperparasitized by
property chain axiom: parasite of
IAO_0000115: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
IAO_0000116: Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: http://eol.org/schema/terms/hyperparasitoidOf
IAO_0000119: https://en.wikipedia.org/wiki/Hyperparasite
has narrow synonym: hyperparasitoid of
has related synonym: epiparasite of
in subset: ro-eco

hyperparasitized by
type: ObjectProperty
sub property of: host of
property chain axiom: parasitized by
IAO_0000115: inverse of hyperparasite of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has related synonym: has epiparasite
has related synonym: has hyperparasite
has related synonym: hyperparasitoidized by
in subset: RO_0002259
in subset: ro-eco

pathogen of
type: ObjectProperty
sub property of: has host
inverse of: has pathogen
IAO_0000115: Inverse of has pathogen
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

has pathogen
type: ObjectProperty
sub property of: host of
IAO_0000115: A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

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

results in movement of
type: ObjectProperty
sub property of: results in changes to anatomical or cellular structure
IAO_0000115: Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

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
IAO_0000115: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

participates in a biotic-biotic interaction with
type: ObjectProperty
sub property of: biotically interacts with
domain: organism
range: organism
IAO_0000117: https://orcid.org/0000-0002-6601-2165
in subset: ro-eco

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
IAO_0000115: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
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'
IAO_0000115: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
IAO_0000115: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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: pending final vetting
IAO_0000115: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
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: pending final vetting
IAO_0000115: a produced_by b iff some process that occurs_in b has_output a.
IAO_0000117: https://orcid.org/0000-0001-9114-8737
in subset: ro-eco

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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: https://orcid.org/0000-0002-6601-2165
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: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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
IAO_0000115: 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: https://orcid.org/0000-0002-6601-2165
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: https://orcid.org/0000-0002-6601-2165
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: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
IAO_0000115: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
IAO_0000115: 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: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
IAO_0000115: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: https://orcid.org/0000-0003-1813-6857
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.
IAO_0000115: 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_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
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-2620-0345
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: 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

is anatomical entity
type: ObjectProperty
domain: anatomical entity
IAO_0000115: This property only applies to anatomical entities.
contributor: https://orcid.org/0000-0001-6677-8489
date: 2024-10-29T09:55:07Z

results in changes to anatomical or cellular structure
type: ObjectProperty
sub property of: has participant
IAO_0000115: p has anatomical participant c iff p has participant c, and c is an anatomical entity
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-09-26T01:08:58Z

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
IAO_0000115: 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
IAO_0000115: 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
IAO_0000115: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

process
type: Class
subclass of: occurrent
IAO_0000115: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
comment: 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
IAO_0000115: 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
IAO_0000115: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
comment: 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
IAO_0000115: 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
IAO_0000115: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
comment: 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
IAO_0000115: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
IAO_0000116: Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

cell
type: Class
subclass of: anatomical structure
IAO_0000115: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
IAO_0000116: CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc.
IAO_0000116: We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.
has db xref: CALOHA:TS-2035
has db xref: FMA:68646
has db xref: GO:0005623
has db xref: KUPO:0000002
has db xref: MESH:D002477
has db xref: VHOG:0001533
has db xref: WBbt:0004017
has db xref: XAO:0003012
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

Axiom
annotated source: cell
annotated property: IAO_0000115
annotated target: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
has db xref: CARO:mah

organism
type: Class
subclass of: material anatomical entity
IAO_0000115: A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome
IAO_0000116: 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'.
IAO_0000116: Includes virus - we will later have a class for cellular organisms.

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
IAO_0000111: curation status specification
IAO_0000114: pending final vetting
IAO_0000115: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
IAO_0000116: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
IAO_0000117: PERSON:Bill Bug
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO_0000119: OBI_0000266

quality
type: Class
subclass of: specifically dependent continuant
IAO_0000115: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: IAO_0000115
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has db xref: PATOC:GVG

linear
type: Class
subclass of: quality
IAO_0000115: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
id: PATO:0001199

Axiom
annotated source: linear
annotated property: IAO_0000115
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
has db xref: ISBN:0881923214

anatomical structure
type: Class
subclass of: material anatomical entity
IAO_0000115: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010825
has db xref: AEO:0000003
has db xref: BILA:0000003
has db xref: CARO:0000003
has db xref: EHDAA2:0003003
has db xref: EMAPA:0
has db xref: FAO:0000001
has db xref: FMA:305751
has db xref: FMA:67135
has db xref: GAID:781
has db xref: HAO:0000003
has db xref: MA:0003000
has db xref: MESH:D000825
has db xref: SCTID:362889002
has db xref: TAO:0000037
has db xref: TGMA:0001823
has db xref: VHOG:0001759
has db xref: XAO:0003000
has db xref: ZFA:0000037
has db xref: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
id: UBERON:0000061
in subset: common anatomy
in subset: human reference atlas
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: anatomical structure
annotated property: IAO_0000115
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has db xref: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: hasExactSynonym
annotated target: connected biological structure
has db xref: CARO:0000003

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
IAO_0000115: Anatomical entity that has mass.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010264
has db xref: AEO:0000006
has db xref: BILA:0000006
has db xref: CARO:0000006
has db xref: EHDAA2:0003006
has db xref: FMA:67165
has db xref: HAO:0000006
has db xref: TAO:0001836
has db xref: TGMA:0001826
has db xref: VHOG:0001721
id: UBERON:0000465
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: IAO_0000115
annotated target: Anatomical entity that has mass.
has db xref: http://orcid.org/0000-0001-9114-8737

anatomical entity
type: Class
equivalent class: Restriction
  on property: is anatomical entity
  has self: true
subclass of: independent continuant
IAO_0000115: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon 4751
has db xref: AAO:0010841
has db xref: AEO:0000000
has db xref: BFO:0000004
has db xref: BILA:0000000
has db xref: BIRNLEX:6
has db xref: CARO:0000000
has db xref: EHDAA2:0002229
has db xref: FMA:62955
has db xref: HAO:0000000
has db xref: MA:0000001
has db xref: NCIT:C12219
has db xref: TAO:0100000
has db xref: TGMA:0001822
has db xref: UMLS:C1515976
has db xref: WBbt:0000100
has db xref: XAO:0000000
has db xref: ZFA:0100000
id: UBERON:0001062
in subset: common anatomy
in subset: human subset
in subset: mouse subset
in subset: upper level

Axiom
annotated source: anatomical entity
annotated property: IAO_0000115
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has db xref: FMA:62955
has db xref: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: hasDbXref
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

Western Australian Mulga Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:25:21Z
has broad synonym: Western Australia Ecoregion
has db xref: WWF:AA1310
has db xref: https://www.worldwildlife.org/ecoregions/aa1310

Australasia Ecoregion
type: NamedIndividual
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:51:32Z
has db xref: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Tirari-Sturt Stony Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:52:41Z
has broad synonym: Southern central Australia Ecoregion
has db xref: WWF:AA1309
has db xref: https://www.worldwildlife.org/ecoregions/aa1309

Simpson Desert Region
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:54:35Z
has broad synonym: Eastern central Australia Ecoregion
has db xref: WWF:AA1308
has db xref: https://www.worldwildlife.org/ecoregions/aa1308

Pilbara Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T17:56:13Z
has broad synonym: Western Australia Ecoregion
has db xref: WWF:AA1307
has db xref: https://www.worldwildlife.org/ecoregions/aa1307

Carnarvon Xeric Shrublands Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:10:52Z
has broad synonym: Western coast of Australia Ecoregion
has db xref: WWF:AA1301
has db xref: https://www.worldwildlife.org/ecoregions/aa1301

Central Ranges Xeric Shrub Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:12:28Z
has broad synonym: Central Australia Ecoregion
has db xref: WWF:AA1302
has db xref: https://www.worldwildlife.org/ecoregions/aa1302

Gibson Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:15:11Z
has broad synonym: Western central Australia
has db xref: WWF:AA1303
has db xref: https://www.worldwildlife.org/ecoregions/aa1303

The Great Sandy-Tanami Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:17:15Z
has broad synonym: Northwestern Australia
has db xref: WWF:AA1304
has db xref: https://www.worldwildlife.org/ecoregions/aa1304

Great Victoria Desert Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:24:06Z
has broad synonym: Southern Australia Ecoregion
has db xref: WWF:AA1305
has db xref: https://www.worldwildlife.org/ecoregions/aa1305

Nullarbor Plains Xeric Shrubland Ecoregion
type: NamedIndividual
part of: Australasia Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-05T18:26:16Z
has broad synonym: Southern Australia Ecoregion
has db xref: WWF:AA1306
has db xref: https://www.worldwildlife.org/ecoregions/aa1306

Afrotropical Ecoregion
type: NamedIndividual
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:01:41Z
has db xref: https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands

Succulent Karoo Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:02:37Z
has broad synonym: Southern Africa: Southern Namibia into South Africa
has db xref: WWF:AT1322
has db xref: https://www.worldwildlife.org/ecoregions/at1322

Yemen and Saudi Arabia Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:07:38Z
has db xref: WWF:AT1321
has db xref: https://www.worldwildlife.org/ecoregions/at1321
has exact synonym: Arabian Peninsula: Yemen and Saudi Arabia

Yemen, Saudi Arabia, and Oman Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:11:38Z
has db xref: WWF:AT1320
has db xref: https://www.worldwildlife.org/ecoregions/at1320
has exact synonym: Arabian Peninsula: Yemen, Saudi Arabia, and Oman

Somali Montane Xeric Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
created by: https://orcid.org/0000-0002-4366-3088
creation date: 2019-03-06T22:13:00Z
has db xref: WWF:AT1319
has db xref: https://www.worldwildlife.org/ecoregions/at1319
has exact synonym: Somali montane xeric woodlands ecoregion

Socotran Archipelago Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:15:07Z
has broad synonym: Islands east of the Horn of Africa and south of Yemen Ecoregion
has db xref: WWF:AT1318
has db xref: https://www.worldwildlife.org/ecoregions/at1318

Red Sea Coastal Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:18:55Z
has db xref: WWF:AT1317
has db xref: https://www.worldwildlife.org/ecoregions/at1317

Namibian Savanna Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:20:56Z
has db xref: WWF:AT1316
has db xref: https://www.worldwildlife.org/ecoregions/at1316

Namib Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:24:28Z
has broad synonym: Africa: Namibia Ecoregion
has db xref: WWF:AT1315
has db xref: https://www.worldwildlife.org/ecoregions/at1315

Nama Karoo Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:26:15Z
has db xref: WWF:AT1314
has db xref: https://www.worldwildlife.org/ecoregions/at1314

Masai Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:28:43Z
has db xref: WWF:AT1313
has db xref: https://www.worldwildlife.org/ecoregions/at1313

Madagascar Succulent Woodlands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:30:23Z
has db xref: WWF:AT1312
has db xref: https://www.worldwildlife.org/ecoregions/at1312

Madagascar Spiny Thickets Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:31:29Z
has db xref: WWF:AT1311
has db xref: https://www.worldwildlife.org/ecoregions/at1311
has exact synonym: Madagascar spiny desert ecoregion

Kaokoveld Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:39:32Z
has db xref: WWF:AT1310
has db xref: https://www.worldwildlife.org/ecoregions/at1310
has exact synonym: Africa: Coastal Namibia and Angola Ecoregion

Kalahari Xeric Savanna Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:42:47Z
has db xref: WWF:AT1309
has db xref: https://www.worldwildlife.org/ecoregions/at1309

Ile Europa and Bassas da India Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:44:54Z
has db xref: WWF:AT1308
has db xref: https://www.worldwildlife.org/ecoregions/at1308
has exact synonym: Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion

Hobyo Grassland and Shrubland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:46:58Z
has broad synonym: Eastern Africa: Somalia
has db xref: WWF:AT1307
has db xref: https://www.worldwildlife.org/ecoregions/at1307

Oman and United Arab Emirates Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-06T22:54:57Z
has db xref: WWF:AT1306
has db xref: https://www.worldwildlife.org/ecoregions/at1306
has exact synonym: Arabian Peninsula: Oman and United Arab Emirates Ecoregion

Ethiopian Xeric Grasslands and Shrublands Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:08:06Z
has db xref: WWF:AT1305
has db xref: https://www.worldwildlife.org/ecoregions/at1305

Eritrean Coastal Desert Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:11:29Z
has db xref: WWF:AT1304
has db xref: https://www.worldwildlife.org/ecoregions/at1304

East Saharan Montane Xeric Woodland Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:13:33Z
has db xref: WWF:AT1303
has db xref: https://www.worldwildlife.org/ecoregions/at1303
has exact synonym: North central Africa: Eastern Chad and small area of western Sudan

Oman, Yemen, and Saudi Arabia Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:16:12Z
has db xref: WWF:AT1302
has db xref: https://www.worldwildlife.org/ecoregions/at1302
has exact synonym: Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion

Aldabra Island Xeric Scrub Ecoregion
type: NamedIndividual
part of: Afrotropical Ecoregion
creation date: 2019-03-07T00:18:09Z
has db xref: WWF:AT1301
has db xref: https://www.worldwildlife.org/ecoregions/at1301

Indo-Malay Ecoregion
type: NamedIndividual
creation date: 2019-04-26T23:38:50Z
has db xref: deserts-and-xeric-shrublands

Thar Desert
type: NamedIndividual
part of: Indo-Malay Ecoregion
creation date: 2019-04-26T23:40:13Z
has db xref: im1304
has db xref: WWF:IM1304
has related synonym: Southern Asia: Western India into Pakistan

Northwestern Thorn Scrub Forests
type: NamedIndividual
part of: Indo-Malay Ecoregion
creation date: 2019-04-27T00:12:51Z
has db xref: im1303
has db xref: WWF:IM1303
has related synonym: Southern Asia: Eastern India and western Pakistan

Solar radiation
type: NamedIndividual
process has causal agent: Q525
IAO_0000115: Stellar radiation emitted from Sol.

example to be eventually removed
type: NamedIndividual
IAO_0000111: example to be eventually removed

metadata complete
type: NamedIndividual
IAO_0000111: metadata complete
IAO_0000115: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
IAO_0000111: organizational term
IAO_0000115: The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.

ready for release
type: NamedIndividual
IAO_0000111: ready for release
IAO_0000114: pending final vetting
IAO_0000115: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
IAO_0000111: metadata incomplete
IAO_0000115: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
IAO_0000111: uncurated
IAO_0000115: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
IAO_0000111: pending final vetting
IAO_0000115: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

to be replaced with external ontology term
type: NamedIndividual
IAO_0000111: to be replaced with external ontology term
IAO_0000115: Terms with this status should eventually replaced with a term from another ontology.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
IAO_0000111: requires discussion
IAO_0000114: pending final vetting
IAO_0000115: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

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 input
  argument1: eff
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
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 input
  argument1: mf
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
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: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
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: directly positively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
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: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
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: causally downstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

'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: causally upstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y