Plant Gall Ontology
type: Ontology
version IRI: gallont.owl
description: Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.
license: https://creativecommons.org/publicdomain/zero/1.0/
version info: 2024-04-19

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative label
type: AnnotationProperty
IAO_0000111: alternative label
IAO_0000114: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
IAO_0000117: OBO Operations committee
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative term

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

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

description
type: AnnotationProperty

license
type: AnnotationProperty

title
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
label: has exact synonym

has_related_synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative label: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable
RO_0040042: quality
RO_0040042: characteristic
RO_0040042: BFO_0000031
has db xref: BFO:0000050
has OBO namespace: external
has OBO namespace: plant_ontology
has OBO namespace: quality
id: part_of
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam
shorthand: part_of
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative label: has_part
RO_0001900: RO_0001901
has db xref: BFO:0000051
has OBO namespace: external
has OBO namespace: plant_ontology
has OBO namespace: quality
id: has_part
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_part
label: has_part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: preceded by
definition: 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.
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
created by: Laurel_Cooper
creation date: 2013-07-09T14:29:15Z
has db xref: BFO:0000062
has OBO namespace: external
has OBO namespace: plant_ontology
id: preceded_by
in subset: ro-eco
shorthand: preceded_by
comment: 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.
label: preceded_by

Axiom
annotated source: preceded by
annotated property: definition
annotated target: 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.
has db xref: POC:Laurel_Cooper

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
created by: Laurel_Cooper
creation date: 2015-06-04T17:18:40Z
has db xref: BFO:0000063
has OBO namespace: external
has OBO namespace: plant_ontology
id: precedes
in subset: ro-eco
shorthand: precedes

has associate
type: ObjectProperty
range: organism
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-01-24T01:49:45Z
comment: Relationship that specifies which organism is associated with a class.

induced by
type: ObjectProperty
sub property of: symbiotically interacts with

has seasonal maturity
type: ObjectProperty
range: season

has seasonal emergence
type: ObjectProperty
range: season

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer of
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
alternative label: 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.

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: characteristic
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative label: bearer_of
alternative label: is bearer of
RO_0001900: RO_0001901
has db xref: RO:0000053
has OBO namespace: external
id: bearer_of
shorthand: bearer_of
label: has characteristic

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative label: participates_in
has db xref: RO:0000056
has OBO namespace: external
has OBO namespace: plant_ontology
id: participates_in
shorthand: participates_in
label: participates_in

has participant
type: ObjectProperty
domain: occurrent
domain: process
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative label: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
has db xref: RO:0000057
has OBO namespace: external
has OBO namespace: plant_ontology
id: has_participant
shorthand: has_participant
label: has_participant

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative label: function_of
alternative label: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

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

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative label: is role of
alternative label: 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: bearer of
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative label: has_function

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative label: has_quality

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative label: has_role

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

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:30:46Z
has db xref: RO:0002013
has OBO namespace: external
id: has_regulatory_component_activity
shorthand: has_regulatory_component_activity

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:01Z
has db xref: RO:0002014
has OBO namespace: external
id: has_negative_regulatory_component_activity
shorthand: has_negative_regulatory_component_activity
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: 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
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:49:21Z

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
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
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
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:47Z

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

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

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

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
IAO_0000117: David Osumi-Sutherland
alternative label: starts_at_end_of
has db xref: RO:0002087
has OBO namespace: external
id: immediately_preceded_by
shorthand: immediately_preceded_by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: https://orcid.org/0000-0002-7073-9172
IAO_0000117: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: meets
RO_0002575: precedes
has db xref: RO:0002090
has OBO namespace: external
id: immediately_precedes
in subset: ro-eco
shorthand: immediately_precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
IAO_0000114: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
has db xref: RO:0002131
has OBO namespace: external
id: overlaps
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco
shorthand: overlaps

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

only in taxon
type: ObjectProperty
sub property of: in taxon
definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
has db xref: RO:0002160
has OBO namespace: plant_ontology
id: only_in_taxon
shorthand: only_in_taxon
label: only_in_taxon

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
range: organism
property chain axiom: part of
property chain axiom: has part
property chain axiom: develops_from
property chain axiom: capable of
property chain axiom: has developmental contribution from
definition: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
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
has db xref: RO:0002180
has OBO namespace: external
id: has_component
in subset: ro-eco
shorthand: has_component

develops_from
type: ObjectProperty
sub property of: has developmental contribution from
sub property of: developmentally_preceded_by
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
has db xref: RO:0002202
has OBO namespace: plant_ontology
id: develops_from
shorthand: develops_from
label: develops from

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
definition: inverse of develops from

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
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
has db xref: RO:0002211
has OBO namespace: external
id: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
has db xref: RO:0002212
has OBO namespace: external
id: negatively_regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
has db xref: RO:0002213
has OBO namespace: external
id: positively_regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: positively_regulates

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: 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)".
has db xref: RO:0002215
has OBO namespace: external
id: capable_of
in subset: ro-eco
shorthand: capable_of

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: has function in
has db xref: RO:0002216
has OBO namespace: external
id: capable_of_part_of
shorthand: capable_of_part_of

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

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: 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 input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
IAO_0000114: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: consumes
has db xref: RO:0002233
has OBO namespace: external
id: has_input
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco
shorthand: has_input

has developmental contribution from
type: ObjectProperty
sub property of: developmentally_preceded_by
inverse of: developmentally contributes to
domain: anatomical entity
range: anatomical entity
property chain axiom: has part
property chain axiom: develops_from
definition: x has developmental contribution from y iff x has some part z such that z develops from y

developmentally contributes to
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to developmentally contribute to
property chain axiom: develops into
property chain axiom: part of
definition: inverse of has developmental contribution from

developmentally_preceded_by
type: ObjectProperty
sub property of: developmentally related to
inverse of: developmentally succeeded by
domain: continuant
range: continuant
definition: Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
definition: X developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p.
created by: Laurel_Cooper
creation date: 2013-06-27T13:16:56Z
has db xref: RO:0002258
has OBO namespace: plant_ontology
id: developmentally_preceded_by
shorthand: developmentally_preceded_by
label: developmentally preceded by

Axiom
annotated source: developmentally_preceded_by
annotated property: definition
annotated target: X developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p.
has db xref: RO:0002258

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in subset: valid for go gp2term

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
definition: Inverse of developmentally preceded by

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002304
has OBO namespace: external
id: causally_upstream_of,_positive_effect
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: causally_upstream_of,_positive_effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002305
has OBO namespace: external
id: causally_upstream_of,_negative_effect
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: causally_upstream_of,_negative_effect

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

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

evolutionarily related to
type: ObjectProperty
definition: A relationship that holds via some environmental process

ecologically related to
type: ObjectProperty
definition: A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
IAO_0000116: Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
IAO_0000117: 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
definition: A mereological relationship or a topological relationship
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in subset: valid for go gp2term

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

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

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

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: actively involved in
alternative label: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
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
definition: inverse of regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000589: regulated by (processual)
has db xref: RO:0002334
has OBO namespace: external
id: regulated_by
in subset: RO_0002259
shorthand: regulated_by

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002335
has OBO namespace: external
id: negatively_regulated_by
in subset: RO_0002259
shorthand: negatively_regulated_by

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002336
has OBO namespace: external
id: positively_regulated_by
in subset: RO_0002259
shorthand: positively_regulated_by

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

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).

has potential to developmentally contribute to
type: ObjectProperty
sub property of: has developmental potential involving
definition: x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y

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
definition: inverse of upstream of
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002404
has OBO namespace: external
id: causally_downstream_of
shorthand: causally_downstream_of

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
has db xref: RO:0002405
has OBO namespace: external
id: immediately_causally_downstream_of
shorthand: immediately_causally_downstream_of

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

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

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
IAO_0000117: 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: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
has db xref: RO:0002411
has OBO namespace: external
id: causally_upstream_of
in subset: valid for go annotation extension
in subset: valid for gocam
shorthand: causally_upstream_of

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of
has db xref: RO:0002412
has OBO namespace: external
id: immediately_causally_upstream_of
shorthand: immediately_causally_upstream_of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)
has db xref: RO:0002418
has OBO namespace: external
has_related_synonym: affects
id: causally_upstream_of_or_within
shorthand: causally_upstream_of_or_within

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
has db xref: RO:0002427
has OBO namespace: external
id: causally_downstream_of_or_within
in subset: RO_0002259
shorthand: causally_downstream_of_or_within

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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

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

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

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000117: 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
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: binds
alternative label: molecularly binds with

biotically interacts with
type: ObjectProperty
sub property of: ecologically related to
sub property of: interacts with
type: SymmetricProperty
domain: material entity
range: material entity
definition: An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
alternative label: 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
definition: 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

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
alternative label: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

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

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
alternative label: 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
definition: 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

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

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

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

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

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

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

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

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

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

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000117: https://orcid.org/0000-0003-4639-4431
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

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
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
IAO_0000117: https://orcid.org/0000-0002-6601-2165
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
has db xref: RO:0002578
has OBO namespace: external
id: directly_regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_regulates

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: https://orcid.org/0000-0002-6601-2165

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

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

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations
has db xref: RO:0002608
has OBO namespace: external
id: process_has_causal_agent
shorthand: process_has_causal_agent

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
has db xref: RO:0002629
has OBO namespace: external
id: directly_positively_regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_positively_regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
has db xref: RO:0002630
has OBO namespace: external
id: directly_negatively_regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: directly_negatively_regulates

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: 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
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: 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
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: 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
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: https://orcid.org/0000-0003-4639-4431

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

different in magnitude relative to
type: ObjectProperty
domain: quality
range: quality
definition: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.

Axiom
annotated source: different in magnitude relative to
annotated property: definition
annotated target: q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

increased in magnitude relative to
type: ObjectProperty
sub property of: different in magnitude relative to
domain: quality
range: quality
definition: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.

Axiom
annotated source: increased in magnitude relative to
annotated property: definition
annotated target: q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
has db xref: https://orcid.org/0000-0002-6601-2165

has cross section
type: ObjectProperty
definition: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

Axiom
annotated source: has cross section
annotated property: definition
annotated target: s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
has db xref: https://orcid.org/0000-0002-6601-2165

reciprocal of
type: ObjectProperty
definition: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.

Axiom
annotated source: reciprocal of
annotated property: definition
annotated target: q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
has db xref: https://orcid.org/0000-0002-6601-2165

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
IAO_0000112: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
IAO_0000117: https://orcid.org/0000-0001-9625-1899
IAO_0000117: https://orcid.org/0000-0003-2620-0345
IAO_0000232: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
IAO_0000232: See github ticket https://github.com/oborel/obo-relations/issues/497
creation date: 2021-11-08T12:00:00Z
has broad synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599
has db xref: RO:0019000
has OBO namespace: gene_ontology
id: regulates_characteristic
shorthand: regulates_characteristic

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599
has db xref: RO:0019001
has OBO namespace: gene_ontology
id: positively_regulates_characteristic
shorthand: positively_regulates_characteristic

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599
has db xref: RO:0019002
has OBO namespace: gene_ontology
id: negatively_regulates_characteristic
shorthand: negatively_regulates_characteristic

hasDiameterInMm
type: DatatypeProperty
range: decimal
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-27T01:25:52Z

hasLengthInMm
type: DatatypeProperty
range: decimal
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-04-11T14:02:15Z
comment: For use with integral galls

hasHeightInMm
type: DatatypeProperty
range: decimal
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-27T17:30:29Z

entity
type: Class
BFO_0000179: entity
BFO_0000180: Entity
IAO_0000112: Julius Caesar
IAO_0000112: Verdi’s Requiem
IAO_0000112: the Second World War
IAO_0000112: your body mass index
IAO_0000116: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
IAO_0000116: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
IAO_0000600: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: IAO_0000116
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

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

continuant
type: Class
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO_0000179: occurrent
BFO_0000180: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
IAO_0000116: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
IAO_0000116: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
IAO_0000116: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0000116: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
IAO_0000600: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
IAO_0000601: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
IAO_0000601: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
IAO_0000602: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
IAO_0000602: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: IAO_0000116
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: IAO_0000116
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: IAO_0000600
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/077-002

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

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

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

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

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: characteristic
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
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.

temporal region
type: Class
subclass of: occurrent
BFO_0000179: t-region
BFO_0000180: TemporalRegion
IAO_0000116: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
IAO_0000600: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
IAO_0000601: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
IAO_0000601: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
IAO_0000602: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
IAO_0000602: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
IAO_0000602: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: IAO_0000116
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: IAO_0000600
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: IAO_0000601
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: IAO_0000601
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: IAO_0000602
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: IAO_0000602
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: IAO_0000602
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/100-001

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: part of
  all values from: process
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
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
disjoint with: role

realizable
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: realizable
disjoint with: quality
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
label: realizable entity

quality
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: quality

characteristic
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: characteristic
subclass of: Restriction
  on property: has part
  all values from: characteristic
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
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.
label: specifically dependent continuant

role
type: Class
subclass of: realizable
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.

function
type: Class
subclass of: disposition

one-dimensional temporal region
type: Class
subclass of: temporal region
BFO_0000179: 1d-t-region
BFO_0000180: OneDimensionalTemporalRegion
IAO_0000112: the temporal region during which a process occurs.
IAO_0000116: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
IAO_0000600: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
IAO_0000602: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: IAO_0000600
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: IAO_0000602
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
IAO_0010000: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

anatomical space
type: Class
definition: Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

asexual organism
type: Class
subclass of: organism

gonochoristic organism
type: Class
subclass of: organism

season
type: Class
subclass of: one-dimensional temporal region

succulent
type: Class
subclass of: internal quality
definition: A gall trait in which the gall parenchyma is juicy, as in the tissue of some fruits (for example grapes, starfruit).
creator: https://orcid.org/0000-0002-2119-4663
source: https://lccn.loc.gov/2011488555

DEPRECATED plant gall
type: Class
comment: Updated the class definition to reflect that this structure is a response to biotic stress
deprecated: true

emergence hole
type: Class
subclass of: plant anatomical space
definition: An anatomical space that is an opening through which a gall-inhabiting organism has emerged.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-19T19:43:46Z

plant gall cavity
type: Class
subclass of: plant anatomical space
definition: A plant anatomical space that is located inside a gall.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-19T19:44:42Z

kapéllo
type: Class
subclass of: multi-tissue plant structure
subclass of: Restriction
  on property: part of
  some values from: plant gall
definition: A gall structure that is attractive to another organism, usually ants, and which facilitates dispersal of the gall
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-22T01:51:19Z

larval chamber
type: Class
subclass of: cardinal part of multi-tissue plant structure
subclass of: Restriction
  on property: has part
  some values from: nutritive tissue
subclass of: Restriction
  on property: has part
  some values from: larval cavity
definition: A gall structure wherein the gall inducer and/or its associates resides and which includes a portion of nutritive tissue.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-22T01:54:05Z

detached chamber
type: Class
subclass of: larval chamber
definition: A larval chamber that is detached from the plant but enclosed in a cavity.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-22T02:01:48Z

internal quality
type: Class
subclass of: morphology
definition: A quality that inheres in the portion of a gall that is internal.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-23T21:16:13Z

filamentous
type: Class
subclass of: internal quality
definition: A gall trait in which a larval chamber is suspended medially in the parenchyma by radiating plant fibers inside a largely hollow chamber.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T01:32:39Z

monothalamous
type: Class
subclass of: internal quality
disjoint with: polythalamous
definition: An internal gall trait in which a gall has a single larval chamber for the gall-inducing insect.
alternative label: single chambered
alternative label: unilocular
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T01:37:35Z

pithy
type: Class
subclass of: internal quality
definition: An internal gall trait in which the tissue is reminiscent of pith, the relatively soft tissue at the center of a shoot axis.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T01:41:48Z

polythalamous
type: Class
subclass of: internal quality
definition: An internal gall trait in which more than one larval chamber is present for the inducer species.
alternative label: multi-celled
alternative label: multichambered
alternative label: multilocular
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T01:44:34Z

solid
type: Class
subclass of: internal quality
disjoint with: hollow
definition: An internal gall trait in which the gall lacks macroscopic anatomical space(s) that is/are not the larval chamber.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T01:58:04Z

nectarous
type: Class
subclass of: morphology
definition: A gall quality in which a gall has nectaries present.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-24T02:13:52Z

caneliform
type: Class
subclass of: 3-D shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling a canelé, a French pastry.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T00:21:14Z
source: https://en.wikipedia.org/w/index.php

cupuliform
type: Class
subclass of: 3-D shape
definition: A shape inhering in a bearer by virtue of the bearer resembling a cup, with a depression and rim-like edge apically.
alternative label: cup-like
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T00:30:40Z
source: https://lccn.loc.gov/2011488555

echinoform
type: Class
subclass of: 3-D shape
definition: A shape trait in which a gall has radiating, spine-like processes that resemble the spines of a sea urchin (cf. Cidaridae).
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T00:38:13Z

infundibuliform
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer being shaped like a funnel, abruptly widening from a narrow cylindrical part, to a wider distal part.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T00:47:37Z
source: https://lccn.loc.gov/2011488555

lenticular
type: Class
subclass of: spheroid
definition: A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lentil, with convex upper and lower surfaces.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T00:52:58Z
source: lenticular

semiterete
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's appearing semicircular in cross-section, flat on one side, rounded on the other.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T02:03:26Z
source: https://lccn.loc.gov/2011488555

confluent
type: Class
subclass of: spatial pattern
definition: A spatial pattern (or gall arrangement) in which adjacent objects (galls) are positioned in such a way that each gall cannot readily be distinguished as an individual.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T19:44:11Z

linear color gradient
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's being marked with one hue or degree of saturation near one pole and a different hue or degree of saturation at the opposite pole and a color gradient between the two poles.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-25T20:11:58Z

corrugated
type: Class
subclass of: texture
disjoint with: unornamented
definition: A texture quality in which the surface is marked by alternating parallel ridges and grooves.
alternative label: ribbed
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:21:38Z
source: PORO_0000234

crackled
type: Class
subclass of: rough
definition: A texture quality in which the surface is marked by a network of cracks, as in craquelure.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:25:58Z
source: https://en.wikipedia.org/w/index.php

dimpled
type: Class
subclass of: surface feature shape
disjoint with: unornamented
definition: A surface feature shape in which a surface has a dimple, a depression or indentation on a surface.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:30:22Z
source: dimpled

plant gall
type: Class
subclass of: multi-tissue plant structure
definition: A multi-tissue plant structure (PO:0025496) that develops in response to a biotic stress (PSO:0000004).
see also: https://www.inaturalist.org/observations/62135900
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-24T21:38:29Z

faceted
type: Class
subclass of: texture
definition: A texture quality in which a surface is covered or partially by with facets.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:35:23Z

moss-like
type: Class
subclass of: texture
disjoint with: smooth
disjoint with: unornamented
definition: A texture quality in which a surface has the appearance and/or consistency of moss, especially those species in Polytrichaceae (Bryophyta).
alternative label: mossy
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:41:40Z

papery
type: Class
subclass of: texture
definition: A texture quality in which a surface has the consistency and thickness of a paper bag (thin and dry).
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T21:48:32Z

felt-like
type: Class
subclass of: hairy
definition: A quality inhering in a bearer by virtue of the bearer's being covered in short, dense, fine hairs, which give the appearance of felt.
alternative label: felted
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-26T22:01:09Z

pruinose
type: Class
subclass of: coating
disjoint with: unornamented
definition: A coating quality in which a surface is covered in a whitish, powdery film or dust.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-27T00:31:53Z
source: https://en.wikipedia.org/w/index.php

semideciduous
type: Class
subclass of: shedability
definition: A shedability quality in which a part can readily be detached from its location but it normally (in nature) stays attached; detachable.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-27T01:16:14Z

brittle
type: Class
subclass of: flexibility
definition: A structural quality inhering in an object by virtue of the object's susceptibility to breaks, without significant deformation (strain) when subjected to stress.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-06-27T01:41:01Z

DEPRECATED erineum
type: Class
comment: logic needed to be fixed
deprecated: true

blister gall
type: Class
subclass of: plant gall
subclass of: Restriction
  on property: part of
  some values from: leaf
definition: A plant gall that is part of a leaf and which appears as a portion of swollen tissue, similar to a blister.
creator: http://orcid.org/0000-0002-2119-4663
date: 2023-08-01T22:15:28Z
source: https://lccn.loc.gov/41001073

bud gall
type: Class
equivalent class: Class
  intersection of: plant gall
  intersection of: Restriction
    on property: part of
    some values from: bud
subclass of: plant gall
subclass of: Restriction
  on property: part of
  some values from: bud
definition: A plant gall that is located on a bud.
creator: http://orcid.org/0000-0002-2119-4663
date: 2023-08-01T22:23:57Z
source: https://lccn.loc.gov/41001073

bullet gall
type: Class
equivalent class: Class
  intersection of: plant gall
  intersection of: Restriction
    on property: has quality
    some values from: monothalamous
  intersection of: Restriction
    on property: has quality
    some values from: solid
  intersection of: Restriction
    on property: has quality
    some values from: semideciduous
  intersection of: Restriction
    on property: has quality
    some values from: spheroid
subclass of: plant gall
subclass of: Restriction
  on property: has quality
  some values from: monothalamous
subclass of: Restriction
  on property: has quality
  some values from: solid
subclass of: Restriction
  on property: has quality
  some values from: semideciduous
subclass of: Restriction
  on property: has quality
  some values from: spheroid
definition: A plant gall that is monothalamous and solid, with a shape reminiscent of a bullet. Gall is usually subspherical or subelliptical in shape.
creator: http://orcid.org/0000-0002-2119-4663
date: 2023-08-01T22:28:40Z
source: https://lccn.loc.gov/41001073

roly-poly gall
type: Class
equivalent class: Class
  intersection of: plant gall
  intersection of: Restriction
    on property: has part
    some values from: detached chamber
  intersection of: Restriction
    on property: has quality
    some values from: hollow
subclass of: plant gall
subclass of: Restriction
  on property: has part
  some values from: detached chamber
subclass of: Restriction
  on property: has quality
  some values from: hollow
definition: A plant gall that has a detached larval chamber capable of rolling around a hollow chamber located inside the gall.
creator: http://orcid.org/0000-0002-2119-4663
date: 2023-08-02T01:35:34Z
source: https://lccn.loc.gov/41001073

rosette gall
type: Class
subclass of: bud gall
subclass of: anatomical entity
subclass of: Restriction
  on property: has part
  some values from: phyllome
definition: A plant gall that is located on a bud and which consists of layers of scale leaves or similar phyllomes that surround the inducer's chamber.
alternative label: bunch gall
creator: http://orcid.org/0000-0002-2119-4663
date: 2023-08-02T01:43:13Z
source: https://lccn.loc.gov/41001073

Acraspis erinacei (agamic)
type: Class
subclass of: asexual organism
subclass of: Acraspis erinacei
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T19:27:00Z

nutritive tissue
type: Class
subclass of: portion of plant tissue
subclass of: Restriction
  on property: part of
  some values from: larval chamber
creator: http://orcid.org/0000-0002-2119-4663
date: 2024-01-19T02:22:00Z
comment: A portion of plant tissue that is fed upon by a gall inhabitant.

larval cavity
type: Class
subclass of: plant gall cavity
definition: A cavity that is occupied by one or more gall inhabitants.
creator: http://orcid.org/0000-0002-2119-4663
date: 2024-01-19T02:27:40Z

Quercus sect. Quercus
type: Class
subclass of: Quercus
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T01:26:41Z

Disholcaspis quercusglobulus (sexgen)
type: Class
subclass of: gonochoristic organism
subclass of: Disholcaspis quercusglobulus
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T01:28:09Z

Disholcaspis quercusglobulus (agamic)
type: Class
subclass of: asexual organism
subclass of: Disholcaspis quercusglobulus
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T01:28:48Z

Acraspis erinacei (sexgen)
type: Class
subclass of: gonochoristic organism
subclass of: Acraspis erinacei
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T19:27:17Z

Aceria triplacis
type: Class
subclass of: Aceria
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T19:39:17Z

Acraspis gemula
type: Class
subclass of: Acraspis
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-03-25T19:40:19Z

erineum
type: Class
equivalent class: Class
  intersection of: plant gall
  intersection of: Restriction
    on property: has part
    some values from: leaf trichome
  intersection of: Restriction
    on property: induced by
    some values from: Acariformes
subclass of: zoocecidium
subclass of: anatomical entity
subclass of: Restriction
  on property: has part
  some values from: leaf trichome
subclass of: Restriction
  on property: induced by
  some values from: Acariformes
definition: A plant gall that is induced by mites (Acariformes) on leaves and which consists of an area of leaf epidermis that has increased hairiness.
creator: https://orcid.org/0000-0002-2119-4663
date: 2023-08-01T21:56:59Z

plant gall aggregate
type: Class
subclass of: multi-tissue plant structure
subclass of: Restriction
  on property: has part
  some values from: plant gall
definition: A multi-tissue plant structure (PO:0025496) that has as parts multiple individual plant galls (GALLONT:0000025) in ane aggregation.
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-04-11T14:32:57Z
label: plant gall cluster

zoocecidium
type: Class
equivalent class: Class
  intersection of: plant gall
  intersection of: Restriction
    on property: induced by
    some values from: Metazoa
subclass of: plant gall
subclass of: organism
subclass of: Restriction
  on property: induced by
  some values from: Metazoa
definition: A plant gall that is induced by an animal
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-04-15T13:33:50Z
source: 978-94-017-6230-4 9

plant gall abscission zone
type: Class
subclass of: abscission zone
definition: An abscission zone (PO:0000146) that is part of a plant gall.
see also: https://www.inaturalist.org/observations/129032167
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-04-18T13:34:27Z

plant gall dehiscence zone
type: Class
subclass of: dehiscence zone
definition: A dehiscence zone that is part of a plant gall. This zone corresponds to the site of rupture in a plant gall.
see also: https://www.inaturalist.org/observations/179039203
creator: https://orcid.org/0000-0002-2119-4663
date: 2024-04-18T14:16:58Z

molecular_function
type: Class
subclass of: process
disjoint with: biological_process
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has alternative id: GO:0005554
has_exact_synonym: molecular function
has OBO namespace: molecular_function
id: GO:0003674
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim yeast
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
comment: This is the same as GO molecular function
label: gene product or complex activity

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

catalytic activity
type: Class
subclass of: molecular_function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
has db xref: Wikipedia:Enzyme
has_exact_synonym: enzyme activity
has OBO namespace: molecular_function
id: GO:0003824
in subset: goslim agr
in subset: goslim chembl
in subset: goslim flybase ribbon
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant

Axiom
annotated source: catalytic activity
annotated property: definition
annotated target: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
has db xref: GOC:vw
has db xref: ISBN:0198506732

Axiom
annotated source: catalytic activity
annotated property: has_exact_synonym
annotated target: enzyme activity
has db xref: GOC:dph
has db xref: GOC:tb

biological_process
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: molecular_function
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
IAO_0000233: https://github.com/geneontology/go-ontology/issues/24968
created by: jl
creation date: 2012-09-19T15:05:24Z
has alternative id: GO:0000004
has alternative id: GO:0007582
has alternative id: GO:0044699
has db xref: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has OBO namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
comment: A biological process is an evolved process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
label: biological process

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

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
has db xref: Reactome:R-HSA-6788855
has db xref: Reactome:R-HSA-6788867
has_exact_synonym: phosphokinase activity
has OBO namespace: molecular_function
id: GO:0016301
in subset: goslim chembl
in subset: goslim drosophila
in subset: goslim metagenomics
in subset: goslim plant
in subset: goslim yeast
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

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

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

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

transferase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
has db xref: EC:2.-.-.-
has db xref: Reactome:R-HSA-1483089
has db xref: Reactome:R-HSA-1483186
has db xref: Reactome:R-HSA-5668414
has db xref: Reactome:R-HSA-8868783
has OBO namespace: molecular_function
id: GO:0016740
in subset: goslim candida
in subset: goslim chembl
in subset: goslim drosophila
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim mouse
in subset: goslim pir
in subset: goslim plant
in subset: goslim prokaryote
in subset: goslim yeast

Axiom
annotated source: transferase activity
annotated property: definition
annotated target: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
has db xref: ISBN:0198506732

PE is converted to PS by PTDSS2
type: Axiom
annotated source: transferase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-1483089

PC is converted to PS by PTDSS1
type: Axiom
annotated source: transferase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-1483186

TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
type: Axiom
annotated source: transferase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-5668414

TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
type: Axiom
annotated source: transferase activity
annotated property: hasDbXref
annotated target: Reactome:R-HSA-8868783

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity
definition: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
has db xref: EC:2.7.-.-
has OBO namespace: molecular_function
id: GO:0016772
in subset: goslim chembl
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.

Axiom
annotated source: transferase activity, transferring phosphorus-containing groups
annotated property: definition
annotated target: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
has db xref: GOC:jl
has db xref: ISBN:0198506732

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
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
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

root
type: Class
subclass of: organism
has db xref: GC_ID:1
has db xref: PMID:30365038
has db xref: PMID:32761142
has OBO namespace: ncbi_taxonomy
has_related_synonym: all
id: NCBITaxon:1

Axiom
annotated source: root
annotated property: has_related_synonym
annotated target: all
has synonym type: synonym

Aceria
type: Class
subclass of: Eriophyidae

Ecdysozoa
type: Class
subclass of: Protostomia
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:1206794

cellular organisms
type: Class
subclass of: root
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
has_related_synonym: biota
id: NCBITaxon:131567

Axiom
annotated source: cellular organisms
annotated property: has_related_synonym
annotated target: biota
has synonym type: synonym

Disholcaspis
type: Class
subclass of: Cynipini

Disholcaspis quercusglobulus
type: Class
subclass of: Disholcaspis

Acraspis
type: Class
subclass of: Cynipini

Pancrustacea
type: Class
subclass of: Mandibulata
has rank: NCBITaxon clade
has db xref: GC_ID:1
has db xref: PMID:10874751
has db xref: PMID:11557979
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:197562

Mandibulata
type: Class
subclass of: Arthropoda
has rank: NCBITaxon clade
has db xref: GC_ID:1
has db xref: PMID:11557979
has db xref: PMID:9727836
has_exact_synonym: mandibulates
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:197563

Axiom
annotated source: Mandibulata
annotated property: has_exact_synonym
annotated target: mandibulates
has synonym type: OMO_0003003

Acraspis erinacei
type: Class
subclass of: Acraspis

Eukaryota
type: Class
subclass of: cellular organisms
has rank: NCBITaxon superkingdom
has db xref: GC_ID:1
has db xref: PMID:23020233
has db xref: PMID:30257078
has_exact_synonym: eucaryotes
has_exact_synonym: eukaryotes
has OBO namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes
id: NCBITaxon:2759

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eucaryotes
has synonym type: genbank common name

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eukaryotes
has synonym type: OMO_0003003

Axiom
annotated source: Eukaryota
annotated property: has_exact_synonym
annotated target: eukaryotes
has synonym type: common name

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eucaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukarya
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: Eukaryotae
has synonym type: synonym

Axiom
annotated source: Eukaryota
annotated property: has_related_synonym
annotated target: eukaryotes
has synonym type: blast name

Viridiplantae
type: Class
subclass of: Eukaryota
has rank: NCBITaxon kingdom
has db xref: GC_ID:1
has db xref: PMID:16248873
has db xref: PMID:30257078
has_exact_synonym: Chlorophyta/Embryophyta group
has_exact_synonym: chlorophyte/embryophyte group
has_exact_synonym: green plants
has OBO namespace: ncbi_taxonomy
has_related_synonym: Chlorobionta
has_related_synonym: Chloroplastida
has_related_synonym: green plants
id: NCBITaxon:33090

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: Chlorophyta/Embryophyta group
has synonym type: equivalent name

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: chlorophyte/embryophyte group
has synonym type: equivalent name

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: green plants
has synonym type: OMO_0003003

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: green plants
has synonym type: common name

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chlorobionta
has synonym type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chloroplastida
has synonym type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: green plants
has synonym type: blast name

Opisthokonta
type: Class
subclass of: Eukaryota
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
has_related_synonym: Fungi/Metazoa group
has_related_synonym: opisthokonts
id: NCBITaxon:33154

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: Fungi/Metazoa group
has synonym type: synonym

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: opisthokonts
has synonym type: synonym

Metazoa
type: Class
subclass of: Opisthokonta
has rank: NCBITaxon kingdom
has db xref: GC_ID:1
has_exact_synonym: metazoans
has_exact_synonym: multicellular animals
has OBO namespace: ncbi_taxonomy
has_related_synonym: Animalia
has_related_synonym: animals
id: NCBITaxon:33208

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: metazoans
has synonym type: genbank common name

Axiom
annotated source: Metazoa
annotated property: has_exact_synonym
annotated target: multicellular animals
has synonym type: OMO_0003003

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: Animalia
has synonym type: synonym

Axiom
annotated source: Metazoa
annotated property: has_related_synonym
annotated target: animals
has synonym type: blast name

Bilateria
type: Class
subclass of: Eumetazoa
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:33213

Protostomia
type: Class
subclass of: Bilateria
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:33317

Cecidomyiidae
type: Class
subclass of: Diptera

Fagaceae
type: Class
subclass of: Viridiplantae

Quercus
type: Class
subclass of: Fagaceae

Quercus alba
type: Class
subclass of: Quercus sect. Quercus

Insecta
type: Class
subclass of: Hexapoda
has rank: NCBITaxon class
has db xref: GC_ID:1
has_exact_synonym: true insects
has OBO namespace: ncbi_taxonomy
has_related_synonym: insects
id: NCBITaxon:50557

Axiom
annotated source: Insecta
annotated property: has_exact_synonym
annotated target: true insects
has synonym type: genbank common name

Axiom
annotated source: Insecta
annotated property: has_related_synonym
annotated target: insects
has synonym type: blast name

Eumetazoa
type: Class
subclass of: Metazoa
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:6072

Arthropoda
type: Class
subclass of: Panarthropoda
has rank: NCBITaxon phylum
has db xref: GC_ID:1
has_exact_synonym: arthropods
has OBO namespace: ncbi_taxonomy
has_related_synonym: arthropods
id: NCBITaxon:6656

Axiom
annotated source: Arthropoda
annotated property: has_exact_synonym
annotated target: arthropods
has synonym type: genbank common name

Axiom
annotated source: Arthropoda
annotated property: has_related_synonym
annotated target: arthropods
has synonym type: blast name

Acariformes
type: Class
subclass of: Arthropoda

Hexapoda
type: Class
subclass of: Pancrustacea
has rank: NCBITaxon subphylum
has db xref: GC_ID:1
has_exact_synonym: insects
has OBO namespace: ncbi_taxonomy
has_related_synonym: Atelocerata
has_related_synonym: Tracheata
has_related_synonym: Uniramia
has_related_synonym: hexapods
id: NCBITaxon:6960

Axiom
annotated source: Hexapoda
annotated property: has_exact_synonym
annotated target: insects
has synonym type: genbank common name

Axiom
annotated source: Hexapoda
annotated property: has_related_synonym
annotated target: Atelocerata
has synonym type: in part

Axiom
annotated source: Hexapoda
annotated property: has_related_synonym
annotated target: Tracheata
has synonym type: in part

Axiom
annotated source: Hexapoda
annotated property: has_related_synonym
annotated target: Uniramia
has synonym type: in part

Axiom
annotated source: Hexapoda
annotated property: has_related_synonym
annotated target: hexapods
has synonym type: blast name

Eriophyidae
type: Class
subclass of: Acariformes

Diptera
type: Class
subclass of: Insecta

Cynipidae
type: Class
subclass of: Hymenoptera

Hymenoptera
type: Class
subclass of: Insecta

Cynipini
type: Class
subclass of: Cynipidae

Panarthropoda
type: Class
subclass of: Ecdysozoa
has rank: NCBITaxon clade
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
id: NCBITaxon:88770

solitary
type: Class
subclass of: spatial pattern
definition: Not accompanied by another or others; exclusive of anyone or anything else.

organism
type: Class
subclass of: material entity
IAO_0000111: organism
IAO_0000112: animal
IAO_0000112: fungus
IAO_0000112: plant
IAO_0000112: virus
IAO_0000114: ready for release
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
IAO_0000116: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
IAO_0000116: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
IAO_0000117: GROUP: OBI Biomaterial Branch
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Organism

quality
type: Class
subclass of: characteristic
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
has alternative id: PATO:0000072
has OBO namespace: quality
id: PATO:0000001

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

age
type: Class
subclass of: time
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
has OBO namespace: quality
id: PATO:0000011
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: age
annotated property: definition
annotated target: A time quality inhering in a bearer by virtue of how long the bearer has existed.
has db xref: WordNet:WordNet

color
type: Class
subclass of: morphology
subclass of: optical quality
definition: A composite chromatic quality composed of hue, saturation and intensity parts.
has alternative id: PATO:0000020
has_exact_synonym: colour
has_exact_synonym: relative color
has OBO namespace: quality
id: PATO:0000014
in subset: attribute slim

Axiom
annotated source: color
annotated property: definition
annotated target: A composite chromatic quality composed of hue, saturation and intensity parts.
has db xref: PATOC:GVG

color pattern
type: Class
subclass of: spatial pattern
definition: A chromatic property that is the relative position of different hues or degrees of saturation.
has OBO namespace: quality
id: PATO:0000019
in subset: attribute slim

Axiom
annotated source: color pattern
annotated property: definition
annotated target: A chromatic property that is the relative position of different hues or degrees of saturation.
has db xref: PATOC:GVG

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has OBO namespace: quality
id: PATO:0000051
in subset: attribute slim

Axiom
annotated source: morphology
annotated property: definition
annotated target: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has db xref: PATOC:GVG

shape
type: Class
subclass of: morphology
definition: A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
has alternative id: PATO:0001647
has_exact_synonym: relational shape quality
has OBO namespace: quality
id: PATO:0000052
in subset: attribute slim
comment: Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.

Axiom
annotated source: shape
annotated property: definition
annotated target: A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
has db xref: PATOC:GVG

spatial pattern
type: Class
subclass of: morphology
definition: A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
alternative label: distribution
has alternative id: PATO:0000132
has alternative id: PATO:0001565
has_exact_synonym: distribution
has OBO namespace: quality
has_related_synonym: pattern
id: PATO:0000060
in subset: attribute slim
in subset: hpo slim

Axiom
annotated source: spatial pattern
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
has db xref: PATOC:GVG

pilosity
type: Class
subclass of: texture
definition: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.
has OBO namespace: quality
id: PATO:0000066
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: pilosity
annotated property: definition
annotated target: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.
has db xref: PATOC:GVG

qualitative
type: Class
subclass of: quality
has OBO namespace: quality
id: PATO:0000068
comment: TODO: define this or obsolete it and move children somewhere else.

deviation (from_normal)
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
has OBO namespace: quality
id: PATO:0000069
in subset: attribute slim

Axiom
annotated source: deviation (from_normal)
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
has db xref: PATOC:GVG

amount
type: Class
subclass of: qualitative
subclass of: Restriction
  on property: reciprocal of
  some values from: has number of
definition: The number of entities of this type that are part of the whole organism.
definition: The number of entities of this type that are part of the whole organism. For galls, the number of entities of some type that are part of or located in a whole gall.
has alternative id: PATO:0000053
has alternative id: PATO:0000071
has alternative id: PATO:0001169
has alternative id: PATO:0001226
has_exact_synonym: presence or absence in organism
has_exact_synonym: quantitative
has OBO namespace: quality
has_related_synonym: count in organism
has_related_synonym: number
has_related_synonym: presence
id: PATO:0000070
in subset: attribute slim
comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.

Axiom
annotated source: amount
annotated property: definition
annotated target: The number of entities of this type that are part of the whole organism.
has db xref: PATOC:GVG

Axiom
annotated source: amount
annotated property: definition
annotated target: The number of entities of this type that are part of the whole organism. For galls, the number of entities of some type that are part of or located in a whole gall.
contributor: https://orcid.org/0000-0002-2119-4663

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
has OBO namespace: quality
id: PATO:0000117
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: size
annotated property: definition
annotated target: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
has db xref: WordNet:WordNet

height
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
has OBO namespace: quality
id: PATO:0000119
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: height
annotated property: definition
annotated target: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
has db xref: PATOC:GVG

length
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality which is equal to the distance between two points.
see also: https://github.com/pato-ontology/pato/issues/337
has OBO namespace: quality
id: PATO:0000122
in subset: attribute slim
in subset: mpath slim
in subset: scalar slim
comment: Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.

Axiom
annotated source: length
annotated property: definition
annotated target: A 1-D extent quality which is equal to the distance between two points.
has db xref: PATOC:GVG

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
has alternative id: PATO:0001032
has alternative id: PATO:0001631
has_exact_synonym: location
has_exact_synonym: placement
has_exact_synonym: relational spatial quality
has OBO namespace: quality
id: PATO:0000140
in subset: attribute slim

Axiom
annotated source: position
annotated property: definition
annotated target: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
has db xref: PATOC:GVG

structure
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
has alternative id: PATO:0001452
has broad synonym: conformation
has_exact_synonym: relational structural quality
has OBO namespace: quality
id: PATO:0000141
in subset: attribute slim

Axiom
annotated source: structure
annotated property: definition
annotated target: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
has db xref: PATOC:GVG

Axiom
annotated source: structure
annotated property: hasBroadSynonym
annotated target: conformation
has db xref: VT:1000738

texture
type: Class
subclass of: morphology
definition: A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
has OBO namespace: quality
id: PATO:0000150
in subset: attribute slim

Axiom
annotated source: texture
annotated property: definition
annotated target: A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics.
has db xref: PATOC:GVG

time
type: Class
subclass of: physical quality
definition: A quality in which events occur in sequence.
has OBO namespace: quality
id: PATO:0000165
in subset: attribute slim
in subset: scalar slim

Axiom
annotated source: time
annotated property: definition
annotated target: A quality in which events occur in sequence.
has db xref: PATOC:GVG

young
type: Class
subclass of: age
definition: An age which is relatively low.
RO_0002604: PATO_0000308
has OBO namespace: quality
id: PATO:0000309
in subset: value slim

Axiom
annotated source: young
annotated property: definition
annotated target: An age which is relatively low.
has db xref: PATOC:GVG

black
type: Class
subclass of: color
definition: A color that lacks any hues as parts.
has OBO namespace: quality
id: PATO:0000317
in subset: mpath slim
in subset: value slim

Axiom
annotated source: black
annotated property: definition
annotated target: A color that lacks any hues as parts.
has db xref: PATOC:GVG

green
type: Class
subclass of: color
definition: A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers.
has OBO namespace: quality
id: PATO:0000320
in subset: mpath slim
in subset: value slim

Axiom
annotated source: green
annotated property: definition
annotated target: A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers.
has db xref: Dictionary:http://dictionary.reference.com/

red
type: Class
subclass of: color
definition: A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers.
has OBO namespace: quality
id: PATO:0000322
in subset: mpath slim
in subset: value slim

Axiom
annotated source: red
annotated property: definition
annotated target: A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers.
has db xref: Dictionary:http://dictionary.reference.com/

yellow
type: Class
subclass of: color
definition: A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers.
has OBO namespace: quality
id: PATO:0000324
in subset: mpath slim
in subset: value slim

Axiom
annotated source: yellow
annotated property: definition
annotated target: A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers.
has db xref: Dictionary:http://dictionary.reference.com/

blotchy
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's being marked with irregularly shaped spots or blots of a different hue or degree of saturation.
has_exact_synonym: blotched
has OBO namespace: quality
id: PATO:0000329
in subset: value slim

Axiom
annotated source: blotchy
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's being marked with irregularly shaped spots or blots of a different hue or degree of saturation.
has db xref: Dictionary.com:Dictionary.com

irregular spatial pattern
type: Class
subclass of: spatial pattern
definition: A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency.
RO_0002604: PATO_0000440
has OBO namespace: quality
id: PATO:0000330
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: irregular spatial pattern
annotated property: definition
annotated target: A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency.
has db xref: PATOC:GVG

spotted
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's being marked with a round area of different hue or degree of saturation.
has OBO namespace: quality
id: PATO:0000333
in subset: value slim

Axiom
annotated source: spotted
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's being marked with a round area of different hue or degree of saturation.
has db xref: PATOC:GVG

curved
type: Class
subclass of: curvature
definition: A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend.
has narrow synonym: bowing
has OBO namespace: quality
has_related_synonym: curled
id: PATO:0000406
in subset: cell quality
in subset: value slim

Axiom
annotated source: curved
annotated property: definition
annotated target: A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend.
has db xref: WordNet:WordNet

oblate
type: Class
subclass of: spheroid
definition: A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting an equatorial diameter greater than its polar diameter.
has_exact_synonym: oblate spheroid
has OBO namespace: quality
id: PATO:0000409
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: oblate
annotated property: definition
annotated target: A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting an equatorial diameter greater than its polar diameter.
has db xref: WordNet:WordNet

circular
type: Class
subclass of: elliptic
definition: A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
has OBO namespace: quality
has_related_synonym: round
has_related_synonym: rounded
id: PATO:0000411
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: circular
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
has db xref: thefreedictionary.com:thefreedictionary.com

glabrous
type: Class
subclass of: pilosity
disjoint with: hairy
definition: A pilosity quality inhering in a bearer by virtue of the bearer's lack of hairs or bristles.
has OBO namespace: quality
has_related_synonym: hairless
id: PATO:0000453
in subset: mpath slim
in subset: value slim

Axiom
annotated source: glabrous
annotated property: definition
annotated target: A pilosity quality inhering in a bearer by virtue of the bearer's lack of hairs or bristles.
has db xref: PATOC:CJM
has db xref: PATOC:GVG

hairy
type: Class
subclass of: pilosity
disjoint with: unornamented
definition: A pilosity quality inhering in a bearer by virtue of the bearer's being covered with hair or hairlike projections.
has OBO namespace: quality
id: PATO:0000454
in subset: mpath slim
in subset: value slim

Axiom
annotated source: hairy
annotated property: definition
annotated target: A pilosity quality inhering in a bearer by virtue of the bearer's being covered with hair or hairlike projections.
has db xref: PATOC:GVG

normal
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
RO_0002604: PATO_0000460
has OBO namespace: quality
has_related_synonym: average
id: PATO:0000461
in subset: abnormal slim
in subset: mpath slim
in subset: value slim

Axiom
annotated source: normal
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
has db xref: PATOC:GVG

conspicuous
type: Class
subclass of: conspicuousness
definition: A quality inhering in a bearer by virtue of being clearly visible.
definition: A quality inhering in a bearer by virtue of being clearly visible. For a gall, a quality in which the gall is clearly visible externally.
RO_0002604: inconspicuous
has OBO namespace: quality
has_related_synonym: distinct
id: PATO:0000463
in subset: mpath slim
in subset: value slim

Axiom
annotated source: conspicuous
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of being clearly visible.
has db xref: thefreedictionary:thefreedictionary

Axiom
annotated source: conspicuous
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of being clearly visible. For a gall, a quality in which the gall is clearly visible externally.
contributor: https://orcid.org/0000-0002-2119-4663

inconspicuous
type: Class
subclass of: conspicuousness
definition: A quality inhering in a bearer by virtue of not being clearly visible.
definition: A quality inhering in a bearer by virtue of not being clearly visible. For a gall, a quality in which the gall is not clearly visible externally.
alternative label: cryptic
RO_0002604: conspicuous
has OBO namespace: quality
has_related_synonym: faint
id: PATO:0000464
in subset: mpath slim
in subset: value slim

Axiom
annotated source: inconspicuous
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of not being clearly visible.
has db xref: thefreedictionary:thefreedictionary

Axiom
annotated source: inconspicuous
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of not being clearly visible. For a gall, a quality in which the gall is not clearly visible externally.
contributor: https://orcid.org/0000-0002-2119-4663

present
type: Class
subclass of: amount
definition: A quality inhering in a bearer by virtue of the bearer's existence.
RO_0002604: PATO_0000462
has OBO namespace: quality
has_related_synonym: present in organism
id: PATO:0000467
in subset: absent slim
in subset: value slim

Axiom
annotated source: present
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's existence.
has db xref: PATOC:GVG

increased amount
type: Class
equivalent class: Class
  intersection of: amount
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: present
subclass of: increased quality
definition: An amount which is relatively high.
RO_0002604: PATO_0001997
has alternative id: PATO:0000420
has alternative id: PATO:0000650
has_exact_synonym: increased number
has_exact_synonym: present in greater numbers in organism
has_exact_synonym: supernumerary
has OBO namespace: quality
has_related_synonym: accessory
has_related_synonym: increased
id: PATO:0000470
in subset: value slim

Axiom
annotated source: increased amount
annotated property: definition
annotated target: An amount which is relatively high.
has db xref: PATOC:GVG

increased height
type: Class
equivalent class: Class
  intersection of: height
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: height
subclass of: increased size
definition: A height which is relatively high.
RO_0002604: PATO_0000569
has OBO namespace: quality
has_related_synonym: tall
id: PATO:0000570
in subset: value slim

Axiom
annotated source: increased height
annotated property: definition
annotated target: A height which is relatively high.
has db xref: PATOC:GVG

increased length
type: Class
equivalent class: Class
  intersection of: length
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: length
subclass of: increased size
definition: A length quality which is relatively large.
RO_0002604: PATO_0000574
has_exact_synonym: long
has OBO namespace: quality
id: PATO:0000573
in subset: value slim

Axiom
annotated source: increased length
annotated property: definition
annotated target: A length quality which is relatively large.
has db xref: PATOC:GVG

increased size
type: Class
equivalent class: Class
  intersection of: size
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: size
subclass of: increased object quality
definition: A size quality which is relatively high.
RO_0002604: PATO_0000587
has alternative id: PATO:0001202
has OBO namespace: quality
has_related_synonym: big
has_related_synonym: enlarged
has_related_synonym: expanded
has_related_synonym: great
has_related_synonym: large
id: PATO:0000586
in subset: value slim

Axiom
annotated source: increased size
annotated property: definition
annotated target: A size quality which is relatively high.
has db xref: PATOC:GVG

increased width
type: Class
equivalent class: Class
  intersection of: width
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: increased size
subclass of: width
definition: A width which is relatively large.
RO_0002604: PATO_0000599
has OBO namespace: quality
has_related_synonym: broad
has_related_synonym: wide
has_related_synonym: wide/broad
id: PATO:0000600
in subset: value slim

Axiom
annotated source: increased width
annotated property: definition
annotated target: A width which is relatively large.
has db xref: PATOC:GVG

exserted
type: Class
subclass of: protruding
definition: A quality inhering in a bearer by virtue of the bearer's protruding or projecting from the body.
has OBO namespace: quality
has_related_synonym: prolapse
has_related_synonym: prolapsed
id: PATO:0000623
in subset: value slim

Axiom
annotated source: exserted
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's protruding or projecting from the body.
has db xref: sdvc:sdvc

rough
type: Class
subclass of: texture
disjoint with: smooth
definition: A texture quality inhering in a bearer by virtue of the bearer's irregular surface.
RO_0002604: smooth
has alternative id: PATO:0001616
has_exact_synonym: coarse
has OBO namespace: quality
id: PATO:0000700
in subset: mpath slim
in subset: value slim

Axiom
annotated source: rough
annotated property: definition
annotated target: A texture quality inhering in a bearer by virtue of the bearer's irregular surface.
has db xref: PATOC:GVG

smooth
type: Class
subclass of: texture
disjoint with: spiny
definition: A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities.
RO_0002604: rough
has OBO namespace: quality
id: PATO:0000701
in subset: mpath slim
in subset: value slim

Axiom
annotated source: smooth
annotated property: definition
annotated target: A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities.
has db xref: PATOC:GVG

width
type: Class
subclass of: 1-D extent
definition: A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
see also: https://github.com/pato-ontology/pato/issues/337
has OBO namespace: quality
has_related_synonym: breadth
id: PATO:0000921
in subset: attribute slim
in subset: scalar slim
comment: Width often refers to the dimension that is greater than the extent in only one of the other two orthogonal dimensions, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion.

Axiom
annotated source: width
annotated property: definition
annotated target: A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
has db xref: PATOC:GVG

sharpness
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point.
has_exact_synonym: apiculate
has OBO namespace: quality
id: PATO:0000944
in subset: attribute slim
in subset: cell quality

Axiom
annotated source: sharpness
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point.
has db xref: PATOC:GVG

elliptic
type: Class
subclass of: superelliptic
definition: A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
has_exact_synonym: ellipse-shaped
has_exact_synonym: ellipsoid
has_exact_synonym: elliptical
has OBO namespace: quality
has_related_synonym: oval
has_related_synonym: ovoid
id: PATO:0000947
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: elliptic
annotated property: definition
annotated target: A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
has db xref: PATOC:GVG

brown
type: Class
subclass of: color
definition: A color consisting of dark orange, red, of very low intensity.
has OBO namespace: quality
id: PATO:0000952
in subset: mpath slim
in subset: value slim

Axiom
annotated source: brown
annotated property: definition
annotated target: A color consisting of dark orange, red, of very low intensity.
has db xref: Wikipedia:http://en.wikipedia.org/wiki/Brown

pink
type: Class
subclass of: red
definition: Red color having medium to high brightness and low to moderate saturation.
has OBO namespace: quality
id: PATO:0000954
in subset: mpath slim
in subset: value slim

Axiom
annotated source: pink
annotated property: definition
annotated target: Red color having medium to high brightness and low to moderate saturation.
has db xref: PATOC:MAH

opacity
type: Class
subclass of: optical quality
definition: An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
has OBO namespace: quality
id: PATO:0000957
in subset: attribute slim

Axiom
annotated source: opacity
annotated property: definition
annotated target: An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
has db xref: PATOC:GVG

opaque
type: Class
subclass of: opacity
definition: A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
RO_0002604: PATO_0000964
has_exact_synonym: non-transparent
has OBO namespace: quality
has_related_synonym: clouding
has_related_synonym: cloudy
id: PATO:0000963
in subset: mpath slim
in subset: value slim

Axiom
annotated source: opaque
annotated property: definition
annotated target: A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
has db xref: PATOC:GVG

permeability
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
has OBO namespace: quality
id: PATO:0000970
in subset: attribute slim
in subset: disposition slim
in subset: scalar slim

Axiom
annotated source: permeability
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
has db xref: Biology-online:Biology-online

permeable
type: Class
subclass of: permeability
definition: A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
RO_0002604: PATO_0000983
has OBO namespace: quality
has_related_synonym: porous
id: PATO:0000982
in subset: disposition slim
in subset: value slim

Axiom
annotated source: permeable
annotated property: definition
annotated target: A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
has db xref: Biology-online:Biology-online

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has alternative id: PATO:0002079
has db xref: Wikipedia:Physical_property
has_exact_synonym: relational physical quality
has OBO namespace: quality
id: PATO:0001018
in subset: attribute slim

Axiom
annotated source: physical quality
annotated property: definition
annotated target: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has db xref: PATOC:GVG

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
has alternative id: PATO:0001237
has alternative id: PATO:0001238
has db xref: snap:Quality
has_exact_synonym: monadic quality of a continuant
has_exact_synonym: multiply inhering quality of a physical entity
has_exact_synonym: quality of a continuant
has_exact_synonym: quality of a single physical entity
has_exact_synonym: quality of an object
has_exact_synonym: quality of continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has OBO namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

Axiom
annotated source: physical object quality
annotated property: definition
annotated target: A quality which inheres in a continuant.
has db xref: PATOC:GVG

light brown
type: Class
subclass of: brown
definition: A color consisting of brown hue and high brightness.
has OBO namespace: quality
id: PATO:0001246
in subset: mpath slim
in subset: value slim

Axiom
annotated source: light brown
annotated property: definition
annotated target: A color consisting of brown hue and high brightness.
has db xref: PATOC:GVG

light green
type: Class
subclass of: green
definition: A color consisting of green hue and high brightness.
has OBO namespace: quality
id: PATO:0001250
in subset: mpath slim
in subset: value slim

Axiom
annotated source: light green
annotated property: definition
annotated target: A color consisting of green hue and high brightness.
has db xref: PATOC:GVG

light yellow
type: Class
subclass of: yellow
definition: A color consisting of yellow hue and high brightness.
has OBO namespace: quality
has_related_synonym: blond
id: PATO:0001264
in subset: mpath slim
in subset: value slim

Axiom
annotated source: light yellow
annotated property: definition
annotated target: A color consisting of yellow hue and high brightness.
has db xref: PATOC:GVG

red brown
type: Class
subclass of: brown
definition: A color consisting of red and brown hue.
has OBO namespace: quality
id: PATO:0001287
in subset: mpath slim
in subset: value slim

Axiom
annotated source: red brown
annotated property: definition
annotated target: A color consisting of red and brown hue.
has db xref: PATOC:GVG

optical quality
type: Class
subclass of: quality of interaction of a substance with electromagnetic radiation
definition: An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
has OBO namespace: quality
id: PATO:0001300
in subset: attribute slim

Axiom
annotated source: optical quality
annotated property: definition
annotated target: An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
has db xref: PATOC:GVG

amorphous
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
has OBO namespace: quality
id: PATO:0001332
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: amorphous
annotated property: definition
annotated target: A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
has db xref: PATOC:GVG

diameter
type: Class
subclass of: 1-D extent
definition: A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary.
has OBO namespace: quality
id: PATO:0001334
in subset: attribute slim
in subset: mpath slim
in subset: scalar slim

Axiom
annotated source: diameter
annotated property: definition
annotated target: A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary.
has db xref: Wikipedia:http://en.wikipedia.org/wiki/Diameter

translucent
type: Class
subclass of: opacity
definition: A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity.
has OBO namespace: quality
id: PATO:0001354
in subset: value slim

Axiom
annotated source: translucent
annotated property: definition
annotated target: A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity.
has db xref: PATOC:GVG

rugose
type: Class
subclass of: rough
subclass of: surface feature shape
definition: A surface feature shape quality inhering in a bearer by virtue of the bearer's having many wrinkles or creases on the surface.
has OBO namespace: quality
id: PATO:0001359
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: rugose
annotated property: definition
annotated target: A surface feature shape quality inhering in a bearer by virtue of the bearer's having many wrinkles or creases on the surface.
has db xref: PATOC:GVG

warty
type: Class
subclass of: rough
definition: A texture quality inhering in a bearer by virtue of the bearer's being covered with warts or projections that resemble warts resulting in a hard rough surface.
has OBO namespace: quality
id: PATO:0001361
in subset: mpath slim
in subset: value slim

Axiom
annotated source: warty
annotated property: definition
annotated target: A texture quality inhering in a bearer by virtue of the bearer's being covered with warts or projections that resemble warts resulting in a hard rough surface.
has db xref: PATOC:GVG

fragile
type: Class
subclass of: fragility
disjoint with: non-fragile
definition: A structural quality inhering in a bearer by virtue of the bearer's disposition to being easily damaged or destroyed.
RO_0002604: non-fragile
has OBO namespace: quality
id: PATO:0001362
in subset: disposition slim
in subset: value slim

Axiom
annotated source: fragile
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's disposition to being easily damaged or destroyed.
has db xref: WordNet:WordNet

spiny
type: Class
subclass of: texture
subclass of: surface feature shape
disjoint with: unornamented
definition: A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface.
has OBO namespace: quality
id: PATO:0001365
in subset: cell quality
in subset: value slim

Axiom
annotated source: spiny
annotated property: definition
annotated target: A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface.
has db xref: PATOC:GVG

viscid
type: Class
subclass of: coating
definition: A coating quality which is sticky or clammy.
has OBO namespace: quality
id: PATO:0001370
in subset: value slim

Axiom
annotated source: viscid
annotated property: definition
annotated target: A coating quality which is sticky or clammy.
has db xref: PATOC:GVG

spindle-shaped
type: Class
subclass of: convex 3-D shape
definition: A shape quality inhering in a bearer by virtue of the bearer's resembling a long tapered rod.
has OBO namespace: quality
id: PATO:0001409
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: spindle-shaped
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's resembling a long tapered rod.
has db xref: Biology-online:Biology-online

sharp
type: Class
subclass of: sharpness
definition: A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge.
has OBO namespace: quality
id: PATO:0001419
in subset: cell quality
in subset: value slim

Axiom
annotated source: sharp
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge.
has db xref: PATOC:GVG

attachment quality
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity.
has OBO namespace: quality
id: PATO:0001435
in subset: attribute slim
in subset: relational slim

Axiom
annotated source: attachment quality
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity.
has db xref: PATOC:GVG

sessile (sensu botany)
type: Class
subclass of: attachment quality
definition: An attachment quality inhering in a flower by virtue of the bearer's lacking a stalk, as in flowers or leaves that grow directly from the stem.
has OBO namespace: quality
id: PATO:0001436
in subset: relational slim
in subset: value slim

Axiom
annotated source: sessile (sensu botany)
annotated property: definition
annotated target: An attachment quality inhering in a flower by virtue of the bearer's lacking a stalk, as in flowers or leaves that grow directly from the stem.
has db xref: Wikipedia:http://en.wikipedia.org/wiki/Sessility_(botany)

pedicellate
type: Class
subclass of: attachment quality
definition: A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle.
has OBO namespace: quality
id: PATO:0001438
in subset: relational slim
in subset: value slim

Axiom
annotated source: pedicellate
annotated property: definition
annotated target: A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle.
has db xref: MedTerms:MedTerms

increased position
type: Class
equivalent class: Class
  intersection of: position
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: position
subclass of: increased object quality
definition: A position which is relatively high.
RO_0002604: PATO_0001476
has OBO namespace: quality
has_related_synonym: high position
id: PATO:0001475
in subset: value slim

Axiom
annotated source: increased position
annotated property: definition
annotated target: A position which is relatively high.
has db xref: PATOC:GVG

spongy
type: Class
subclass of: internal quality
subclass of: structure
subclass of: Restriction
  on property: has part
  some values from: permeable
definition: A structural quality inhering in a bearer by virtue of the bearer's resembling a sponge in elasticity, absorbency, or porousness.
alternative label: sponge-like
has OBO namespace: quality
id: PATO:0001480
in subset: mpath slim
in subset: value slim

Axiom
annotated source: spongy
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's resembling a sponge in elasticity, absorbency, or porousness.
has db xref: Answers.com:Answers.com

senescent
type: Class
subclass of: age
definition: A time quality inhering in a bearer by virtue of the bearer's growing old; aging.
has OBO namespace: quality
id: PATO:0001487
in subset: mpath slim
in subset: value slim

Axiom
annotated source: senescent
annotated property: definition
annotated target: A time quality inhering in a bearer by virtue of the bearer's growing old; aging.
has db xref: answers.com:answers.com

spherical
type: Class
subclass of: spheroid
subclass of: Restriction
  on property: has cross section
  some values from: circular
definition: A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter).
has alternative id: PATO:0000408
has_exact_synonym: globular
has OBO namespace: quality
has_related_synonym: rotund
id: PATO:0001499
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: spherical
annotated property: definition
annotated target: A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter).
has db xref: WordNet:WordNet

tapered
type: Class
subclass of: sharp
definition: A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end.
alternative label: taper
has_exact_synonym: taper
has OBO namespace: quality
id: PATO:0001500
in subset: cell quality
in subset: value slim

Axiom
annotated source: tapered
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end.
has db xref: WordNet:WordNet

mono-colored
type: Class
subclass of: color pattern
definition: A color pattern inhering in a bearer by virtue of the bearer's having one hue.
alternative label: uniformly colored
has_exact_synonym: evenly colored
has_exact_synonym: homogeneously colored
has_exact_synonym: uniformly colored
has OBO namespace: quality
has_related_synonym: homogenously pigmented
id: PATO:0001532
in subset: value slim

Axiom
annotated source: mono-colored
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of the bearer's having one hue.
has db xref: PATOC:GVG

multi-colored
type: Class
subclass of: color pattern
definition: A color pattern inhering in a bearer by virtue of bearer's having two or more hues or degrees of saturation.
has_exact_synonym: variegated
has OBO namespace: quality
id: PATO:0001533
in subset: value slim

Axiom
annotated source: multi-colored
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's having two or more hues or degrees of saturation.
has db xref: PATOC:GVG

motley
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's having 3 or more hues or degrees of saturations.
has OBO namespace: quality
id: PATO:0001534
in subset: value slim

Axiom
annotated source: motley
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's having 3 or more hues or degrees of saturations.
has db xref: merriam-webster.:merriam-webster.

dappled
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's being marked with small spots, patches, or specks of hue or degree of saturation differing from that of the background.
has OBO namespace: quality
has_related_synonym: speckled
id: PATO:0001535
in subset: value slim

Axiom
annotated source: dappled
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's being marked with small spots, patches, or specks of hue or degree of saturation differing from that of the background.
has db xref: merriam-webster.:merriam-webster.

flexibility
type: Class
subclass of: quality of a solid
definition: A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
has OBO namespace: quality
id: PATO:0001543
in subset: attribute slim
in subset: disposition slim

Axiom
annotated source: flexibility
annotated property: definition
annotated target: A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
has db xref: merriam-webster:merriam-webster

flexible
type: Class
subclass of: flexibility
definition: A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking.
RO_0002604: PATO_0001545
has_exact_synonym: bendy
has OBO namespace: quality
id: PATO:0001544
in subset: disposition slim
in subset: value slim

Axiom
annotated source: flexible
annotated property: definition
annotated target: A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking.
has db xref: merriam-webster:merriam-webster

quality of a solid
type: Class
subclass of: quality of a substance
definition: A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
has_exact_synonym: solidity
has OBO namespace: quality
id: PATO:0001546
in subset: attribute slim

Axiom
annotated source: quality of a solid
annotated property: definition
annotated target: A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
has db xref: Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm

has number of
type: Class
subclass of: physical object quality
subclass of: Restriction
  on property: reciprocal of
  some values from: amount
definition: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
has db xref: OBO_REL:has_part
has_exact_synonym: extra or missing physical or functional parts
has_exact_synonym: has or lacks parts of type
has_exact_synonym: mereological quality
has_exact_synonym: number of
has OBO namespace: quality
has_related_synonym: cardinality
has_related_synonym: number
id: PATO:0001555
in subset: attribute slim
in subset: relational slim

Axiom
annotated source: has number of
annotated property: definition
annotated target: The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
has db xref: PATOC:CJM

increased permeability
type: Class
equivalent class: Class
  intersection of: permeable
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: permeable
subclass of: increased object quality
definition: A permeability which is relatively high.
RO_0002604: PATO_0001578
has_exact_synonym: high permeability
has OBO namespace: quality
id: PATO:0001577
in subset: disposition slim
in subset: value slim

Axiom
annotated source: increased permeability
annotated property: definition
annotated target: A permeability which is relatively high.
has db xref: PATO:GVG

curvature
type: Class
subclass of: shape
definition: A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
has OBO namespace: quality
id: PATO:0001591
in subset: attribute slim

Axiom
annotated source: curvature
annotated property: definition
annotated target: A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
has db xref: WordNet:WordNet

increased curvature
type: Class
equivalent class: Class
  intersection of: curved
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: curved
subclass of: increased object quality
definition: A curvature which is relatively high.
RO_0002604: PATO_0001593
has OBO namespace: quality
id: PATO:0001592
in subset: value slim

Axiom
annotated source: increased curvature
annotated property: definition
annotated target: A curvature which is relatively high.
has db xref: PATO:GVG

protruding
type: Class
subclass of: physical quality
definition: A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary.
has alternative id: PATO:0001644
has_exact_synonym: protruding
has_exact_synonym: relational protruding quality
has OBO namespace: quality
id: PATO:0001598
in subset: value slim

Axiom
annotated source: protruding
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary.
has db xref: WordNet:WordNet

sparse
type: Class
subclass of: spatial pattern
definition: A spatial pattern inhering in a bearer by virtue of the bearer's being scattered; spread irregularly, and at a distance from each other.
has OBO namespace: quality
id: PATO:0001609
in subset: mpath slim
in subset: value slim
label: scattered

Axiom
annotated source: sparse
annotated property: definition
annotated target: A spatial pattern inhering in a bearer by virtue of the bearer's being scattered; spread irregularly, and at a distance from each other.
has db xref: biology.lsu:biology.lsu

aggregated
type: Class
subclass of: irregular spatial pattern
definition: A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole.
has_exact_synonym: clumped
has_exact_synonym: clustered
has OBO namespace: quality
id: PATO:0001629
in subset: mpath slim
in subset: value slim

Axiom
annotated source: aggregated
annotated property: definition
annotated target: A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole.
has db xref: WordNet:WordNet

fragility
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of the bearer's disposition to being damaged or destroyed.
has OBO namespace: quality
id: PATO:0001662
in subset: attribute slim
in subset: disposition slim
in subset: scalar slim

Axiom
annotated source: fragility
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's disposition to being damaged or destroyed.
has db xref: WordNet:WordNet

1-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
has_exact_synonym: 1-D size
has OBO namespace: quality
id: PATO:0001708
in subset: attribute slim

Axiom
annotated source: 1-D extent
annotated property: definition
annotated target: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
has db xref: PATOC:GVG

increased diameter
type: Class
equivalent class: Class
  intersection of: diameter
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: increased size
subclass of: diameter
definition: A diameter which is relatively large.
RO_0002604: PATO_0001715
has OBO namespace: quality
id: PATO:0001714
in subset: value slim

Axiom
annotated source: increased diameter
annotated property: definition
annotated target: A diameter which is relatively large.
has db xref: PATOC:GVG

non-fragile
type: Class
subclass of: fragility
definition: A structural quality inhering in a bearer by virtue of the bearer's ability to withstand great strain without tearing or breaking.
RO_0002604: fragile
has OBO namespace: quality
has_related_synonym: resilient
has_related_synonym: strong
has_related_synonym: tough
id: PATO:0001716
in subset: attribute slim
in subset: disposition slim

Axiom
annotated source: non-fragile
annotated property: definition
annotated target: A structural quality inhering in a bearer by virtue of the bearer's ability to withstand great strain without tearing or breaking.
has db xref: thefreedictionary.com:thefreedictionary.com

shedability
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process.
has OBO namespace: quality
id: PATO:0001729
in subset: attribute slim
in subset: disposition slim
in subset: relational slim

Axiom
annotated source: shedability
annotated property: definition
annotated target: An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process.
has db xref: PATOC:GVG

deciduous (generic)
type: Class
subclass of: shedability
definition: A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts.
alternative label: detachable
has OBO namespace: quality
id: PATO:0001730
in subset: disposition slim
in subset: relational slim
in subset: value slim

Axiom
annotated source: deciduous (generic)
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts.
has db xref: PATOC:GVG

non-deciduous (any body part)
type: Class
subclass of: shedability
definition: A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part.
alternative label: integral
has OBO namespace: quality
id: PATO:0001732
in subset: disposition slim
in subset: relational slim
in subset: value slim
label: non-deciduous

Axiom
annotated source: non-deciduous (any body part)
annotated property: definition
annotated target: A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part.
has db xref: PATOC:GVG

increased age
type: Class
equivalent class: Class
  intersection of: age
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: age
subclass of: increased object quality
definition: An age which is high relative to the normal or average.
RO_0002604: PATO_0001765
has_exact_synonym: high age
has OBO namespace: quality
id: PATO:0001764
in subset: value slim

Axiom
annotated source: increased age
annotated property: definition
annotated target: An age which is high relative to the normal or average.
has db xref: PATOC:GVG

increased flexibility
type: Class
equivalent class: Class
  intersection of: flexible
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: flexible
subclass of: increased object quality
definition: A flexibility which is relatively high.
RO_0002604: PATO_0001777
has_exact_synonym: high flexibility
has OBO namespace: quality
id: PATO:0001776
in subset: disposition slim
in subset: value slim

Axiom
annotated source: increased flexibility
annotated property: definition
annotated target: A flexibility which is relatively high.
has db xref: PATOC:GVG

swollen
type: Class
subclass of: structure
subclass of: Restriction
  on property: has part
  some values from: increased size
subclass of: Restriction
  on property: has part
  some values from: protruding
definition: A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation.
has narrow synonym: swelling
has OBO namespace: quality
id: PATO:0001851
in subset: mpath slim
in subset: value slim

Axiom
annotated source: swollen
annotated property: definition
annotated target: A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation.
has db xref: thefreedictionary.com:thefreedictionary.com

concave
type: Class
subclass of: concavity
definition: A shape quality in a bearer by virtue of the bearer's curving inward.
RO_0002604: PATO_0001355
has OBO namespace: quality
id: PATO:0001857
in subset: cell quality
in subset: value slim

Axiom
annotated source: concave
annotated property: definition
annotated target: A shape quality in a bearer by virtue of the bearer's curving inward.
has db xref: WordNet:WordNet

spheroid
type: Class
subclass of: convex 3-D shape
definition: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids.
has alternative id: PATO:0001864
has OBO namespace: quality
has_related_synonym: sphericality
id: PATO:0001865
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: spheroid
annotated property: definition
annotated target: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids.
has db xref: Wikipedia:http://en.wikipedia.org/wiki/Spheroid

reniform
type: Class
subclass of: concave 3-D shape
definition: A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney.
has_exact_synonym: kidney-shaped
has OBO namespace: quality
has_related_synonym: bean shaped
id: PATO:0001871
in subset: value slim

Axiom
annotated source: reniform
annotated property: definition
annotated target: A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney.
has db xref: ISBN:0881923214

cylindrical
type: Class
subclass of: convex 3-D shape
subclass of: Restriction
  on property: has cross section
  some values from: circular
definition: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
has alternative id: PATO:0001203
has_exact_synonym: rod-like
has_exact_synonym: rod-shaped
has narrow synonym: tubulate
has OBO namespace: quality
id: PATO:0001873
in subset: cell quality
in subset: value slim

Axiom
annotated source: cylindrical
annotated property: definition
annotated target: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
has db xref: PATOC:MAH

discoid
type: Class
subclass of: cylindrical
definition: A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter.
has_exact_synonym: disc-shaped
has_exact_synonym: disk-shaped
has OBO namespace: quality
id: PATO:0001874
in subset: cell quality
in subset: value slim

Axiom
annotated source: discoid
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter.
has db xref: PATOC:cjm

triangular
type: Class
subclass of: 2-D shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having three angles.
has_exact_synonym: deltoid
has OBO namespace: quality
has_related_synonym: delta shaped
has_related_synonym: triangle
has_related_synonym: triangle-shaped
id: PATO:0001875
in subset: cell quality
in subset: value slim

Axiom
annotated source: triangular
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's having three angles.
has db xref: wordreference:wordreference

lanceolate
type: Class
subclass of: sharp
definition: A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end.
has_exact_synonym: spear-shaped
has OBO namespace: quality
id: PATO:0001877
in subset: cell quality
in subset: value slim

Axiom
annotated source: lanceolate
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end.
has db xref: PATOC:GVG

sigmoid
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped.
alternative label: s-shaped
alternative label: sigmoidal
has_exact_synonym: S-shaped
has_exact_synonym: sigmoidal
has OBO namespace: quality
id: PATO:0001878
in subset: cell quality
in subset: value slim

Axiom
annotated source: sigmoid
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped.
has db xref: PATOC:CJM

clavate
type: Class
subclass of: concave 3-D shape
definition: A concave 3-D shape quality inhering in a bearer by virtue of the bearer's gradually becoming thicker towards the end.
alternative label: club-shaped
has alternative id: PATO:0001797
has_exact_synonym: club-like
has_exact_synonym: club-shaped
has_exact_synonym: clubbed
has OBO namespace: quality
id: PATO:0001883
in subset: value slim

Axiom
annotated source: clavate
annotated property: definition
annotated target: A concave 3-D shape quality inhering in a bearer by virtue of the bearer's gradually becoming thicker towards the end.
has db xref: MP:0000576

botryoidal
type: Class
subclass of: surface feature shape
definition: A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes.
has OBO namespace: quality
id: PATO:0001907
in subset: value slim

Axiom
annotated source: botryoidal
annotated property: definition
annotated target: A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes.
has db xref: PATOC:cvs

surface feature shape
type: Class
subclass of: shape
definition: A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell.
has OBO namespace: quality
id: PATO:0001925
in subset: attribute slim
comment: This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved.

Axiom
annotated source: surface feature shape
annotated property: definition
annotated target: A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell.
has db xref: PATOC:CJM

yellow green
type: Class
subclass of: green
definition: A color consisting of yellow and green hues.
has OBO namespace: quality
id: PATO:0001941
in subset: mpath slim
in subset: value slim

Axiom
annotated source: yellow green
annotated property: definition
annotated target: A color consisting of yellow and green hues.
has db xref: PATOC:GVG

banded
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's exhibiting transverse stripes of one hue or degree of saturation crossing another.
has_exact_synonym: striped
has OBO namespace: quality
id: PATO:0001946
in subset: value slim

Axiom
annotated source: banded
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's exhibiting transverse stripes of one hue or degree of saturation crossing another.
has db xref: ISBN:0881923214

netted
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's being covered with reticulated lines of a different hue or degree of saturation.
has_exact_synonym: net-like
has_exact_synonym: reticulated
has OBO namespace: quality
id: PATO:0001947
in subset: value slim

Axiom
annotated source: netted
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's being covered with reticulated lines of a different hue or degree of saturation.
has db xref: ISBN:0881923214

pointleted
type: Class
subclass of: sharp
definition: A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly in a little point.
has OBO namespace: quality
id: PATO:0001949
in subset: value slim

Axiom
annotated source: pointleted
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly in a little point.
has db xref: ISBN:0881923214

cuneate
type: Class
subclass of: triangular
definition: A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base.
has_exact_synonym: wedge-shaped
has OBO namespace: quality
id: PATO:0001955
in subset: value slim

Axiom
annotated source: cuneate
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base.
has db xref: wordreference:wordreference

lobed
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions.
has OBO namespace: quality
id: PATO:0001979
in subset: mpath slim
in subset: value slim

Axiom
annotated source: lobed
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions.
has db xref: ISBN:0881923214

auriculate
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an ear.
has OBO namespace: quality
id: PATO:0001981
in subset: value slim

Axiom
annotated source: auriculate
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an ear.
has db xref: url:http://www.thefreedictionary.com/auriculate

organismal quality
type: Class
subclass of: physical object quality
definition: A quality that inheres in an entire organism or part of an organism.
has OBO namespace: quality
id: PATO:0001995

Axiom
annotated source: organismal quality
annotated property: definition
annotated target: A quality that inheres in an entire organism or part of an organism.
has db xref: PATOC:CJM

conspicuousness
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of its visibility.
has OBO namespace: quality
id: PATO:0001998
comment: This term was created as a grouping term for the 2 terms "conspicuous" and "inconspicuous". However, it is not clear if these terms should even remain in PATO.

Axiom
annotated source: conspicuousness
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of its visibility.
has db xref: PATOC:MAH

concavity
type: Class
subclass of: shape
definition: Surface shape that refers to the inward or outward curvature of the surface.
has OBO namespace: quality
id: PATO:0002005
in subset: attribute slim

Axiom
annotated source: concavity
annotated property: definition
annotated target: Surface shape that refers to the inward or outward curvature of the surface.
has db xref: PATOC:MAH

2-D shape
type: Class
subclass of: shape
definition: A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
has OBO namespace: quality
has_related_synonym: 2-D projection
has_related_synonym: cross-sectional
id: PATO:0002006
in subset: attribute slim

Axiom
annotated source: 2-D shape
annotated property: definition
annotated target: A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
has db xref: PATOC:CJM

convex 3-D shape
type: Class
subclass of: 3-D shape
subclass of: Restriction
  on property: has cross section
  some values from: 2-D shape
definition: A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
RO_0002604: concave 3-D shape
has db xref: Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png
has OBO namespace: quality
id: PATO:0002007
in subset: attribute slim
comment: Use this term or an is_a child of this term when the entire shape of the object is known.

Axiom
annotated source: convex 3-D shape
annotated property: definition
annotated target: A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
has db xref: PATOC:CJM

concave 3-D shape
type: Class
subclass of: 3-D shape
subclass of: Restriction
  on property: has part
  some values from: concave
definition: A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave.
RO_0002604: convex 3-D shape
has db xref: Image:http://en.wikipedia.org/wiki/Image:Convex_polygon_illustration2.png
has OBO namespace: quality
id: PATO:0002008
in subset: attribute slim

Axiom
annotated source: concave 3-D shape
annotated property: definition
annotated target: A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave.
has db xref: PATOC:CJM

coating
type: Class
subclass of: texture
definition: A texture quality that exists through a liquid cover on the surface of the bearer.
has OBO namespace: quality
id: PATO:0002012
in subset: value slim

Axiom
annotated source: coating
annotated property: definition
annotated target: A texture quality that exists through a liquid cover on the surface of the bearer.
has db xref: Wikipedia:Wikipedia

structure, cavities
type: Class
subclass of: structure
definition: A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
has OBO namespace: quality
id: PATO:0002014
in subset: attribute slim

Axiom
annotated source: structure, cavities
annotated property: definition
annotated target: A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
has db xref: PATOC:GVG

pale pink
type: Class
subclass of: pink
definition: Pink color having high brightness and low saturation.
has OBO namespace: quality
id: PATO:0002020

Axiom
annotated source: pale pink
annotated property: definition
annotated target: Pink color having high brightness and low saturation.
has db xref: PATOC:GVG

conical
type: Class
subclass of: convex 3-D shape
definition: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers).
has db xref: Image:http://upload.wikimedia.org/wikipedia/commons/d/d2/Cone_3d.png
has_exact_synonym: cone-shaped
has OBO namespace: quality
id: PATO:0002021
in subset: value slim

Axiom
annotated source: conical
annotated property: definition
annotated target: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers).
has db xref: Wikipedia:http://en.wikipedia.org/wiki/Cone_(geometry)

increased fragility
type: Class
equivalent class: Class
  intersection of: fragile
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: fragile
subclass of: increased object quality
definition: A fragility which is relatively high.
RO_0002604: PATO_0002056
contributor: 0000-0002-2061-091X
creation date: 2009-03-26T04:01:37Z
has OBO namespace: quality
id: PATO:0002055
in subset: disposition slim
in subset: value slim

Axiom
annotated source: increased fragility
annotated property: definition
annotated target: A fragility which is relatively high.
has db xref: PATOC:GVG

columnar
type: Class
subclass of: shape
definition: A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical.
contributor: 0000-0002-2061-091X
creation date: 2009-07-01T01:44:06Z
has OBO namespace: quality
id: PATO:0002063
in subset: cell quality
in subset: mpath slim
in subset: value slim

Axiom
annotated source: columnar
annotated property: definition
annotated target: A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical.
has db xref: PATOC:me

hollow
type: Class
subclass of: internal quality
subclass of: structure, cavities
definition: A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
contributor: 0000-0002-2061-091X
creation date: 2009-09-18T02:19:20Z
has OBO namespace: quality
id: PATO:0002078
in subset: value slim

Axiom
annotated source: hollow
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
has db xref: url:http://www.merriam-webster.com/dictionary/hollow

papillary
type: Class
subclass of: shape
subclass of: exserted
definition: A quality inhering in a bearer by virtue of the bearer's resembling small nipple like projection.
contributor: 0000-0002-2061-091X
creation date: 2009-10-05T03:04:52Z
has OBO namespace: quality
id: PATO:0002108
in subset: mpath slim
in subset: value slim

Axiom
annotated source: papillary
annotated property: subClassOf
annotated target: shape
comment: probably not the right class for galls with nipple-like projections

Axiom
annotated source: papillary
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's resembling small nipple like projection.
has db xref: PATO:GVG

quality of a substance
type: Class
subclass of: physical quality
definition: A quality inhering in a bearer by virtue of its constitution.
contributor: 0000-0002-2061-091X
creation date: 2010-03-15T04:35:27Z
has OBO namespace: quality
id: PATO:0002198
in subset: attribute slim

Axiom
annotated source: quality of a substance
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of its constitution.
has db xref: PATOC:GVG

falciform
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle.
contributor: 0000-0002-2061-091X
creation date: 2010-07-08T01:57:46Z
has_exact_synonym: falcate
has_exact_synonym: hooked
has_exact_synonym: scythe-shaped
has_exact_synonym: sickle-shaped
has_exact_synonym: unciform
has_exact_synonym: uncinate
has OBO namespace: quality
id: PATO:0002215
in subset: value slim

Axiom
annotated source: falciform
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle.
has db xref: merriam-webster:http://www.merriam-webster.com/dictionary/falciform

subcylindrical
type: Class
subclass of: cylindrical
definition: A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
contributor: 0000-0002-2061-091X
creation date: 2010-07-13T04:22:30Z
has OBO namespace: quality
id: PATO:0002226
in subset: value slim

Axiom
annotated source: subcylindrical
annotated property: definition
annotated target: A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
has db xref: url:http://www.thefreedictionary.com/Subcylindrical

acuminate
type: Class
subclass of: tapered
definition: A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point.
contributor: 0000-0002-2061-091X
creation date: 2010-07-15T09:03:18Z
has OBO namespace: quality
id: PATO:0002228
in subset: value slim

Axiom
annotated source: acuminate
annotated property: definition
annotated target: A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point.
has db xref: url:http://www.thefreedictionary.com/acuminate

teardrop-shaped
type: Class
subclass of: convex 3-D shape
definition: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling falling drop.
contributor: 0000-0002-2061-091X
creation date: 2010-07-23T02:31:11Z
has_exact_synonym: drop shaped
has OBO namespace: quality
id: PATO:0002240
in subset: value slim

Axiom
annotated source: teardrop-shaped
annotated property: definition
annotated target: A convex 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling falling drop.
has db xref: url:wordnetweb.princeton.edu/perl/webwn

3-D shape
type: Class
subclass of: shape
definition: A shape that inheres in a 3 dimensional entity.
contributor: 0000-0002-2061-091X
creation date: 2010-10-05T12:31:16Z
has OBO namespace: quality
id: PATO:0002266

Axiom
annotated source: 3-D shape
annotated property: definition
annotated target: A shape that inheres in a 3 dimensional entity.
has db xref: PATOC:OREGON

marbled
type: Class
subclass of: multi-colored
definition: Multicolored quality inhering in a bearer by virtue of the bearer's being colored with a variegated pattern resembling marble,.
contributor: 0000-0002-2061-091X
creation date: 2010-11-16T11:17:32Z
has OBO namespace: quality
id: PATO:0002273
in subset: value slim

Axiom
annotated source: marbled
annotated property: definition
annotated target: Multicolored quality inhering in a bearer by virtue of the bearer's being colored with a variegated pattern resembling marble,.
has db xref: url:http://www.oed.com/

mottled
type: Class
subclass of: multi-colored
definition: Multicolored quality inhering in a bearer by virtue of the bearer's being dappled with spots, patches, or blotches of different colors.
contributor: 0000-0002-2061-091X
creation date: 2010-11-16T11:22:57Z
has OBO namespace: quality
id: PATO:0002274
in subset: value slim

Axiom
annotated source: mottled
annotated property: definition
annotated target: Multicolored quality inhering in a bearer by virtue of the bearer's being dappled with spots, patches, or blotches of different colors.
has db xref: url:http://www.oed.com/

barred
type: Class
subclass of: multi-colored
definition: A color pattern inhering in a bearer by virtue of bearer's exhibiting vertical bars of one hue or degree of saturation crossing another.
contributor: 0000-0002-2061-091X
creation date: 2010-11-16T11:30:40Z
has OBO namespace: quality
id: PATO:0002276
in subset: value slim

Axiom
annotated source: barred
annotated property: definition
annotated target: A color pattern inhering in a bearer by virtue of bearer's exhibiting vertical bars of one hue or degree of saturation crossing another.
has db xref: PATOC:WD

tubular
type: Class
subclass of: cylindrical
subclass of: hollow
definition: A cylindrical shape that is hollow.
contributor: 0000-0002-2061-091X
creation date: 2011-06-08T06:33:50Z
has_exact_synonym: tube like
has_exact_synonym: tube-shaped
has_exact_synonym: tubulate
has OBO namespace: quality
id: PATO:0002299

Axiom
annotated source: tubular
annotated property: definition
annotated target: A cylindrical shape that is hollow.
has db xref: PATOC:GVG

increased quality
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: deviation (from_normal)
subclass of: Restriction
  on property: increased in magnitude relative to
  some values from: normal
definition: A quality that has a value that is increased compared to normal or average.
RO_0002604: PATO_0002301
contributor: 0000-0002-2061-091X
creation date: 2011-06-16T06:39:43Z
has OBO namespace: quality
id: PATO:0002300

Axiom
annotated source: increased quality
annotated property: definition
annotated target: A quality that has a value that is increased compared to normal or average.
has db xref: PATOC:GVG

increased object quality
type: Class
equivalent class: Class
  intersection of: physical object quality
  intersection of: Restriction
    on property: increased in magnitude relative to
    some values from: normal
subclass of: physical object quality
subclass of: increased quality
definition: A quality of an object that has a value that is increased compared to normal or average.
RO_0002604: PATO_0002303
contributor: 0000-0002-2061-091X
creation date: 2011-06-16T06:54:01Z
has OBO namespace: quality
id: PATO:0002305

Axiom
annotated source: increased object quality
annotated property: definition
annotated target: A quality of an object that has a value that is increased compared to normal or average.
has db xref: PATOC:GVG

fimbriated
type: Class
subclass of: shape
definition: Having a fringe or border of hairlike or fingerlike projections.
contributor: 0000-0002-2061-091X
creation date: 2011-09-22T03:52:11Z
has OBO namespace: quality
id: PATO:0002311
in subset: value slim

Axiom
annotated source: fimbriated
annotated property: definition
annotated target: Having a fringe or border of hairlike or fingerlike projections.
has db xref: PATO:WS

superelliptic
type: Class
subclass of: 2-D shape
definition: A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
contributor: 0000-0002-2061-091X
creation date: 2011-10-12T12:45:16Z
has_exact_synonym: Lamé curve
has OBO namespace: quality
id: PATO:0002318

Axiom
annotated source: superelliptic
annotated property: definition
annotated target: A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
has db xref: wiktionary:superellipse

tholiform
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped.
alternative label: dome-like
alternative label: hemispheroid
contributor: 0000-0002-2061-091X
creation date: 2012-01-31T02:32:14Z
has OBO namespace: quality
id: PATO:0002335
in subset: value slim

Axiom
annotated source: tholiform
annotated property: definition
annotated target: A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped.
has db xref: PATOC:dd

hispid
type: Class
subclass of: hairy
definition: A quality of being covered with stiff or rough hairs.
contributor: 0000-0002-2061-091X
creation date: 2012-01-31T02:51:37Z
has OBO namespace: quality
id: PATO:0002339
in subset: value slim

Axiom
annotated source: hispid
annotated property: definition
annotated target: A quality of being covered with stiff or rough hairs.
has db xref: PATOC:GVG

hispidulous
type: Class
subclass of: hispid
definition: A quality of being minutely hispid.
contributor: 0000-0002-2061-091X
creation date: 2012-01-31T02:53:21Z
has OBO namespace: quality
id: PATO:0002340
in subset: value slim

Axiom
annotated source: hispidulous
annotated property: definition
annotated target: A quality of being minutely hispid.
has db xref: PATOC:DD

arachnose
type: Class
subclass of: hairy
definition: A quality inhering in a bearer by virtue of the bearer's being characterized by fine, entangled hairs giving the appearance of cobweb.
contributor: 0000-0002-2061-091X
creation date: 2012-01-31T03:49:00Z
has OBO namespace: quality
id: PATO:0002344
in subset: value slim

Axiom
annotated source: arachnose
annotated property: definition
annotated target: A quality inhering in a bearer by virtue of the bearer's being characterized by fine, entangled hairs giving the appearance of cobweb.
has db xref: PATOC:DD

fusiform
type: Class
subclass of: spindle-shaped
definition: Having a spindle-like shape that is wide in the middle and tapers at both ends.
contributor: 0000-0002-2061-091X
creation date: 2012-12-07T05:43:25Z
has OBO namespace: quality
id: PATO:0002400
in subset: mpath slim
in subset: value slim

Axiom
annotated source: fusiform
annotated property: definition
annotated target: Having a spindle-like shape that is wide in the middle and tapers at both ends.
has db xref: wikipedia:wikipedia

yellow brown
type: Class
subclass of: brown
definition: A color consisting of yellow and brown hue.
contributor: 0000-0002-2061-091X
creation date: 2012-12-17T10:55:51Z
has OBO namespace: quality
id: PATO:0002411
in subset: value slim

Axiom
annotated source: yellow brown
annotated property: definition
annotated target: A color consisting of yellow and brown hue.
has db xref: PATOC:GVG

knobbled
type: Class
subclass of: surface feature shape
disjoint with: unornamented
definition: A surface feature shape having numerous very small circular rounded projections or protuberances.
alternative label: pebbled
alternative label: tuberculose
contributor: 0000-0002-2061-091X
creation date: 2013-01-29T09:15:53Z
has OBO namespace: quality
id: PATO:0002427
in subset: value slim

Axiom
annotated source: knobbled
annotated property: definition
annotated target: A surface feature shape having numerous very small circular rounded projections or protuberances.
has db xref: thefreedictionary.com:thefreedictionary.com

ornamentation
type: Class
subclass of: surface feature shape
definition: A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures.
contributor: 0000-0002-2061-091X
creation date: 2013-01-29T10:57:42Z
has OBO namespace: quality
id: PATO:0002440
in subset: disposition slim

Axiom
annotated source: ornamentation
annotated property: definition
annotated target: A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures.
has db xref: PATOC:GVG

unornamented
type: Class
subclass of: ornamentation
definition: A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures.
RO_0002604: PATO_0002441
contributor: 0000-0002-2061-091X
creation date: 2013-01-29T11:00:20Z
has OBO namespace: quality
id: PATO:0002442
in subset: value slim

Axiom
annotated source: unornamented
annotated property: definition
annotated target: A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures.
has db xref: PATOC:AD

pear shaped
type: Class
subclass of: convex 3-D shape
definition: Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com
contributor: https://orcid.org/0000-0003-3162-7490
creation date: 2014-09-09T12:30:02Z
has OBO namespace: quality
id: PATO:0005002
in subset: value slim
label: pear-shaped

Axiom
annotated source: pear shaped
annotated property: definition
annotated target: Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com
has db xref: PATOC:WD

subelliptical
type: Class
subclass of: superelliptic
definition: A shape that is almost an ellipse.
contributor: https://orcid.org/0000-0003-3162-7490
creation date: 2014-09-09T12:36:15Z
has OBO namespace: quality
id: PATO:0005004
in subset: value slim

Axiom
annotated source: subelliptical
annotated property: definition
annotated target: A shape that is almost an ellipse.
has db xref: PATOC:WD

subspherical
type: Class
subclass of: spheroid
definition: A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical.
alternative label: globose
alternative label: globular
contributor: https://orcid.org/0000-0003-3162-7490
creation date: 2014-09-25T15:16:25Z
has OBO namespace: quality
id: PATO:0005014
in subset: value slim

Axiom
annotated source: subspherical
annotated property: definition
annotated target: A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical.
has db xref: PATOC:WD

flared
type: Class
subclass of: shape
definition: A shape quality inhering in a bearer by virtue of the bearer being expanded laterally and or opened outward in shape.
date: 2018-11-19T21:49:07Z
contributor: https://orcid.org/0000-0001-5208-3432
has OBO namespace: quality
id: PATO:0040022

quality of interaction of a substance with electromagnetic radiation
type: Class
subclass of: quality of a substance
definition: A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
has OBO namespace: quality
id: PATO:0070060
in subset: attribute slim

Axiom
annotated source: quality of interaction of a substance with electromagnetic radiation
annotated property: definition
annotated target: A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength.
has db xref: https://orcid.org/0000-0002-5111-7263

whole plant
type: Class
subclass of: plant structure
definition: A plant structure (PO:0005679) which is a whole organism.
has broad synonym: genet (broad)
has broad synonym: ramet (broad)
has db xref: PO_GIT:538
has db xref: PO_GIT:69
has_exact_synonym: planta entera (Spanish, exact)
has_exact_synonym: 植物体全体 (Japanese, exact)
has narrow synonym: bush (narrow)
has narrow synonym: frutex (narrow)
has narrow synonym: frutices (narrow, plural)
has narrow synonym: gametophyte (narrow)
has narrow synonym: herb (narrow)
has narrow synonym: liana (narrow)
has narrow synonym: prothalli (narrow, plural)
has narrow synonym: prothallium (narrow)
has narrow synonym: prothallus (narrow)
has narrow synonym: shrub (narrow)
has narrow synonym: sporophyte (narrow)
has narrow synonym: suffrutex (narrow)
has narrow synonym: suffrutices (narrow, plural)
has narrow synonym: tree (narrow)
has narrow synonym: vine (narrow)
has narrow synonym: woody clump (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: clonal colony (related)
has_related_synonym: colony (related)
id: PO:0000003
in subset: TraitNet
in subset: reference
comment: Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280).

Axiom
annotated source: whole plant
annotated property: definition
annotated target: A plant structure (PO:0005679) which is a whole organism.
has db xref: POC:curators

Axiom
annotated source: whole plant
annotated property: has_exact_synonym
annotated target: planta entera (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: whole plant
annotated property: has_exact_synonym
annotated target: 植物体全体 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: frutex (narrow)

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: frutices (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: prothalli (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: prothallus (narrow)

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: suffrutex (narrow)

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: suffrutices (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: whole plant
annotated property: hasNarrowSynonym
annotated target: woody clump (narrow)

vascular leaf primordium
type: Class
subclass of: phyllome primordium
subclass of: Restriction
  on property: part of
  some values from: vegetative shoot apex
subclass of: Restriction
  on property: develops_from
  some values from: vascular leaf anlagen
definition: A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025).
has db xref: PO_GIT:466
has_exact_synonym: leaf primordium (exact)
has_exact_synonym: portion of vascular leaf primordium tissue (exact)
has_exact_synonym: primordio de hoja (Spanish, exact)
has_exact_synonym: vascular leaf primordia (exact, plural)
has_exact_synonym: 葉原基 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000017

Axiom
annotated source: vascular leaf primordium
annotated property: definition
annotated target: A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: vascular leaf primordium
annotated property: has_exact_synonym
annotated target: primordio de hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vascular leaf primordium
annotated property: has_exact_synonym
annotated target: vascular leaf primordia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: vascular leaf primordium
annotated property: has_exact_synonym
annotated target: 葉原基 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

gynoecium primordium
type: Class
subclass of: floral organ primordium
definition: A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
has db xref: PO_GIT:465
has_exact_synonym: pistil primordium (exact)
has_exact_synonym: portion of gynoecium primordium tissue (exact)
has_exact_synonym: primordio de gineceo (Spanish, exact)
has_exact_synonym: 雌蕊原基(可視的） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000019
comment: Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030).

Axiom
annotated source: gynoecium primordium
annotated property: definition
annotated target: A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).
has db xref: POC:curators

Axiom
annotated source: gynoecium primordium
annotated property: has_exact_synonym
annotated target: primordio de gineceo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: gynoecium primordium
annotated property: has_exact_synonym
annotated target: 雌蕊原基(可視的） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

vascular system
type: Class
subclass of: portion of vascular tissue
subclass of: Restriction
  on property: part of
  some values from: whole plant
subclass of: Restriction
  on property: participates in
  some values from: sporophyte development stage
disjoint with: plant cell
disjoint with: plant organ
disjoint with: cardinal organ part
disjoint with: collective plant organ structure
definition: A maximal portion of vascular tissue (PO:0009015) in a whole plant (PO:0000003), collective plant structure (PO:0025497), multi-tissue plant structure (PO:0025496), or cardinal part of multi-tissue plant structure (PO:0025498).
has db xref: PO_GIT:50
has_exact_synonym: sistema vascular (Spanish, exact)
has_exact_synonym: vasculature (exact)
has_exact_synonym: 維管束系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000034
in subset: TraitNet
comment: A vascular system consist of the totality of the portions of vascular tissue in their specific arrangement in a plant structure. May include other portions of plant tissue or plant cells (PO:0009002) of other types, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).

Axiom
annotated source: vascular system
annotated property: definition
annotated target: A maximal portion of vascular tissue (PO:0009015) in a whole plant (PO:0000003), collective plant structure (PO:0025497), multi-tissue plant structure (PO:0025496), or cardinal part of multi-tissue plant structure (PO:0025498).
has db xref: ISBN:0471245208
has db xref: ISBN:0716710072
has db xref: POC:curators

Axiom
annotated source: vascular system
annotated property: has_exact_synonym
annotated target: sistema vascular (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vascular system
annotated property: has_exact_synonym
annotated target: vasculature (exact)

Axiom
annotated source: vascular system
annotated property: has_exact_synonym
annotated target: 維管束系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf vascular system
type: Class
subclass of: phyllome vascular system
subclass of: Restriction
  on property: part of
  some values from: vascular leaf
definition: A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a vascular leaf (PO:0009025).
has db xref: PO_GIT:41
has db xref: PO_GIT:50
has_exact_synonym: sistema vascular de la hoja (Spanish, exact)
has_exact_synonym: 葉維管系 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: leaf venation (related)
id: PO:0000036
in subset: Maize

Axiom
annotated source: leaf vascular system
annotated property: definition
annotated target: A phyllome vascular system (PO:0025206) that includes the totality of the portions of vascular tissue in their specific arrangement in a vascular leaf (PO:0009025).
has db xref: POC:Ramona_Walls

Axiom
annotated source: leaf vascular system
annotated property: has_exact_synonym
annotated target: sistema vascular de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf vascular system
annotated property: has_exact_synonym
annotated target: 葉維管系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot axis apex
type: Class
subclass of: shoot axis
definition: A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
has db xref: PO_GIT:234
has_exact_synonym: &#225pice del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート頂、茎頂 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000037
in subset: reference

Axiom
annotated source: shoot axis apex
annotated property: definition
annotated target: A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127).
has db xref: POC:curators

Axiom
annotated source: shoot axis apex
annotated property: has_exact_synonym
annotated target: &#225pice del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot axis apex
annotated property: has_exact_synonym
annotated target: シュート頂、茎頂 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf lamina epidermis
type: Class
equivalent class: Class
  intersection of: leaf epidermis
  intersection of: Restriction
    on property: part of
    some values from: leaf lamina
subclass of: leaf epidermis
subclass of: Restriction
  on property: part of
  some values from: leaf lamina
definition: A portion of leaf epidermis (PO:0006016) that is part of a leaf lamina (PO:0020039).
has_exact_synonym: epidermis de la l&#225mina de la hoja (Spanish, exact)
has_exact_synonym: 葉身表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000047
comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: leaf lamina epidermis
annotated property: definition
annotated target: A portion of leaf epidermis (PO:0006016) that is part of a leaf lamina (PO:0020039).
has db xref: POC:curators

Axiom
annotated source: leaf lamina epidermis
annotated property: has_exact_synonym
annotated target: epidermis de la l&#225mina de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf lamina epidermis
annotated property: has_exact_synonym
annotated target: 葉身表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf lamina vascular system
type: Class
subclass of: vascular system
subclass of: Restriction
  on property: part of
  some values from: leaf vascular system
subclass of: Restriction
  on property: part of
  some values from: leaf lamina
definition: A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a leaf lamina (PO:0020039).
has db xref: PO_GIT:41
has_exact_synonym: sistema vascular de la l&#225mina de la hoja (Spanish, exact)
has_exact_synonym: 葉身維管系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000048

Axiom
annotated source: leaf lamina vascular system
annotated property: definition
annotated target: A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a leaf lamina (PO:0020039).
has db xref: POC:Ramona_Walls

Axiom
annotated source: leaf lamina vascular system
annotated property: has_exact_synonym
annotated target: sistema vascular de la l&#225mina de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf lamina vascular system
annotated property: has_exact_synonym
annotated target: 葉身維管系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

petiole epidermis
type: Class
equivalent class: Class
  intersection of: leaf epidermis
  intersection of: Restriction
    on property: part of
    some values from: petiole
subclass of: leaf epidermis
subclass of: Restriction
  on property: part of
  some values from: petiole
definition: A portion of leaf epidermis (PO:0006016) that is part of a petiole (PO:0020038).
has_exact_synonym: epidermis del pec&#237olo (Spanish, exact)
has_exact_synonym: 葉柄表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000051
comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: petiole epidermis
annotated property: definition
annotated target: A portion of leaf epidermis (PO:0006016) that is part of a petiole (PO:0020038).
has db xref: POC:Ramona_Walls
has db xref: TAIR_curator:Katica_Ilic

Axiom
annotated source: petiole epidermis
annotated property: has_exact_synonym
annotated target: epidermis del pec&#237olo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: petiole epidermis
annotated property: has_exact_synonym
annotated target: 葉柄表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

bud
type: Class
subclass of: shoot system
subclass of: Restriction
  on property: participates in
  some values from: bud development stage
definition: An undeveloped shoot system (PO:0009006).
has db xref: PO_GIT:124
has_exact_synonym: yema (Spanish, exact)
has_exact_synonym: 芽 (Japanese, exact)
has narrow synonym: adventitious bud (narrow)
has OBO namespace: plant_anatomy
id: PO:0000055
in subset: TraitNet

Axiom
annotated source: bud
annotated property: definition
annotated target: An undeveloped shoot system (PO:0009006).
has db xref: POC:curators

Axiom
annotated source: bud
annotated property: has_exact_synonym
annotated target: yema (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: bud
annotated property: has_exact_synonym
annotated target: 芽 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: bud
annotated property: hasNarrowSynonym
annotated target: adventitious bud (narrow)

shoot axis epidermis
type: Class
equivalent class: Class
  intersection of: shoot system epidermis
  intersection of: Restriction
    on property: part of
    some values from: shoot axis
subclass of: shoot system epidermis
subclass of: Restriction
  on property: part of
  some values from: shoot axis
definition: A portion of shoot system epidermis (PO:0006035) that is part of a shoot axis (PO:0025029).
has_exact_synonym: epidermis del eje del tallo (Spanish, exact)
has_exact_synonym: シュート軸表皮 (Japanese, exact)
has narrow synonym: branch epidermis (narrow)
has OBO namespace: plant_anatomy
id: PO:0000112
comment: Can occur on a stem or branch.

Axiom
annotated source: shoot axis epidermis
annotated property: definition
annotated target: A portion of shoot system epidermis (PO:0006035) that is part of a shoot axis (PO:0025029).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: shoot axis epidermis
annotated property: has_exact_synonym
annotated target: epidermis del eje del tallo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot axis epidermis
annotated property: has_exact_synonym
annotated target: シュート軸表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

nectary epidermis
type: Class
equivalent class: Class
  intersection of: shoot system epidermis
  intersection of: Restriction
    on property: part of
    some values from: nectary
subclass of: shoot system epidermis
subclass of: Restriction
  on property: part of
  some values from: nectary
definition: A portion of shoot system epidermis (PO:0006035) that is part of a nectary (PO:0009035) .
has_exact_synonym: epidermis del nectario (Spanish, exact)
has_exact_synonym: 蜜腺表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000207

Axiom
annotated source: nectary epidermis
annotated property: definition
annotated target: A portion of shoot system epidermis (PO:0006035) that is part of a nectary (PO:0009035) .
has db xref: POC:Ramona_Walls

Axiom
annotated source: nectary epidermis
annotated property: has_exact_synonym
annotated target: epidermis del nectario (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: nectary epidermis
annotated property: has_exact_synonym
annotated target: 蜜腺表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

peripheral zone
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: part of
  some values from: shoot apical meristem
definition: A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
has_exact_synonym: zona perif&#233rica (Spanish, exact)
has_exact_synonym: 周辺帯 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: peripheral meristem (related)
id: PO:0000225

Axiom
annotated source: peripheral zone
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division.
has db xref: ISBN:0521288959
has db xref: TAIR_curator:Leonore_Reiser

Axiom
annotated source: peripheral zone
annotated property: has_exact_synonym
annotated target: zona perif&#233rica (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: peripheral zone
annotated property: has_exact_synonym
annotated target: 周辺帯 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

flower meristem
type: Class
subclass of: reproductive shoot apical meristem
definition: A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
has alternative id: PO:0006329
has alternative id: PO:0006373
has alternative id: PO:0006374
has alternative id: PO:0025091
has_exact_synonym: floral meristem (exact)
has_exact_synonym: mersitema floral (Spanish, exact)
has_exact_synonym: 花芽分裂組織 (Japanese, exact)
has narrow synonym: Poaceae floret meristem (narrow)
has narrow synonym: ear floret meristem (narrow)
has narrow synonym: floret meristem (narrow)
has narrow synonym: tassel floret meristem (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: floral apical meristem (related)
id: PO:0000229
comment: In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).

Axiom
annotated source: flower meristem
annotated property: definition
annotated target: A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395).
has db xref: Gramene:Pankaj_Jaiswal
has db xref: POC:curators

Axiom
annotated source: flower meristem
annotated property: has_exact_synonym
annotated target: mersitema floral (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: flower meristem
annotated property: has_exact_synonym
annotated target: 花芽分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

trichome
type: Class
subclass of: plant structure
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: plant epidermis
subclass of: Restriction
  on property: develops_from
  some values from: plant epidermal initial cell
definition: A unicellular or multicellular plant structure (PO:0009011) that forms a non-sclerified outgrowth from the epidermis (PO:0005679).
has alternative id: PO:0004510
has broad synonym: barb trichome (broad)
has broad synonym: bristle (broad)
has db xref: PO_GIT:207
has_exact_synonym: tricoma (Spanish, exact)
has_exact_synonym: 毛茸、糸状体、毛 (Japanese, exact)
has narrow synonym: capilli (narrow, plural)
has narrow synonym: capillus (narrow)
has narrow synonym: cilia (narrow, plural)
has narrow synonym: cilium (narrow)
has narrow synonym: glochid (narrow)
has narrow synonym: glochidia (narrow, plural)
has narrow synonym: glochidium (narrow)
has narrow synonym: hair (narrow)
has narrow synonym: lepides (narrow, plural)
has narrow synonym: lepis (narrow)
has narrow synonym: non-secretory trichome (narrow)
has narrow synonym: scale (narrow)
has narrow synonym: squama (narrow)
has narrow synonym: squamae (narrow, plural)
has narrow synonym: squamella (narrow)
has narrow synonym: squamellae (narrow, plural)
has narrow synonym: squamule (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: seta (related)
has_related_synonym: setae (related)
id: PO:0000282
in subset: TraitNet
comment: This class is the union of unicellular trichome (PO:0025537) and multicellular trichome (PO:0025162). A trichome can vary in length and shape and may be branched or unbranched. It may be glandular or non-secretory.

Axiom
annotated source: trichome
annotated property: definition
annotated target: A unicellular or multicellular plant structure (PO:0009011) that forms a non-sclerified outgrowth from the epidermis (PO:0005679).
has db xref: PMID:19939948
has db xref: POC:curators

Axiom
annotated source: trichome
annotated property: hasBroadSynonym
annotated target: barb trichome (broad)

Axiom
annotated source: trichome
annotated property: hasBroadSynonym
annotated target: bristle (broad)

Axiom
annotated source: trichome
annotated property: has_exact_synonym
annotated target: tricoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: trichome
annotated property: has_exact_synonym
annotated target: 毛茸、糸状体、毛 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: capilli (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: capillus (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: cilia (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: cilium (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: glochid (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: glochidia (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: glochidium (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: hair (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: lepides (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: lepis (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: scale (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: squama (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: squamae (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: squamella (narrow)

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: squamellae (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: trichome
annotated property: hasNarrowSynonym
annotated target: squamule (narrow)

Axiom
annotated source: trichome
annotated property: has_related_synonym
annotated target: seta (related)

Axiom
annotated source: trichome
annotated property: has_related_synonym
annotated target: setae (related)

plant epidermal initial cell
type: Class
subclass of: initial cell
subclass of: Restriction
  on property: part of
  some values from: plant epidermis
definition: An initial cell (PO:0004011) that is part of an plant epidermis (PO:0005679) and gives rise to specialized cells.
has_exact_synonym: c&#233lula inicial de la epidermis (Spanish, exact)
has_exact_synonym: epidermal initial (exact)
has_exact_synonym: 表皮始原細胞 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0000349
in subset: CL

Axiom
annotated source: plant epidermal initial cell
annotated property: definition
annotated target: An initial cell (PO:0004011) that is part of an plant epidermis (PO:0005679) and gives rise to specialized cells.
has db xref: PO:cooperl
has db xref: TAIR_curator:Leonore_Reiser

Axiom
annotated source: plant epidermal initial cell
annotated property: has_exact_synonym
annotated target: c&#233lula inicial de la epidermis (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant epidermal initial cell
annotated property: has_exact_synonym
annotated target: 表皮始原細胞 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

inflorescence development stage
type: Class
subclass of: reproductive shoot system development stage
definition: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
has db xref: GRO:0007157
has db xref: PO_GIT:517
has OBO namespace: plant_structure_development_stage
has_related_synonym: panicle development (related)
id: PO:0001083

Axiom
annotated source: inflorescence development stage
annotated property: definition
annotated target: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
has db xref: POC:Laurel_Cooper

Axiom
annotated source: inflorescence development stage
annotated property: has_related_synonym
annotated target: panicle development (related)
has db xref: GRO:0007157

meristematic cell
type: Class
subclass of: native plant cell
definition: A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
has db xref: CL:0000034
has db xref: PO_GIT:272
has_exact_synonym: c&#233lula meristem&#225tica (Spanish, exact)
has_exact_synonym: stem cell (exact)
has_exact_synonym: 分裂組織細胞 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0004010
in subset: CL

Axiom
annotated source: meristematic cell
annotated property: definition
annotated target: A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall.
has db xref: ISBN:0471245208
has db xref: POC:Laurel_Cooper

Axiom
annotated source: meristematic cell
annotated property: has_exact_synonym
annotated target: c&#233lula meristem&#225tica (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: meristematic cell
annotated property: has_exact_synonym
annotated target: 分裂組織細胞 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

initial cell
type: Class
subclass of: meristematic cell
definition: A meristematic cell (PO:0004010) that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.
has alternative id: PO:0000070
has db xref: PO_GIT:272
has_exact_synonym: c&#233lula inicial (Spanish, exact)
has_exact_synonym: initial (exact)
has_exact_synonym: meristemoid (exact)
has_exact_synonym: 始原細胞 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: stem cell (related)
id: PO:0004011
in subset: CL
comment: Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic.

Axiom
annotated source: initial cell
annotated property: definition
annotated target: A meristematic cell (PO:0004010) that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.
has db xref: ISBN:0471245208

Axiom
annotated source: initial cell
annotated property: has_exact_synonym
annotated target: c&#233lula inicial (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: initial cell
annotated property: has_exact_synonym
annotated target: 始原細胞 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

vascular bundle
type: Class
subclass of: portion of vascular tissue
definition: A portion of vascular tissue (PO:0009015) that is a unit strand of the vascular system (PO:0000034) and has as part xylem (PO:0005352) or phloem (PO:0005417).
has db xref: PO_GIT:431
has_exact_synonym: haz vascular (Spanish, exact)
has_exact_synonym: vein (exact)
has_exact_synonym: 維管束 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0005020
in subset: Maize
in subset: TraitNet
comment: May also contain portions of ground tissue (PO:0025059). The bundle sheath (PO:0006023) can also be part of a vascular bundle, if it is present.

Axiom
annotated source: vascular bundle
annotated property: definition
annotated target: A portion of vascular tissue (PO:0009015) that is a unit strand of the vascular system (PO:0000034) and has as part xylem (PO:0005352) or phloem (PO:0005417).
has db xref: POC:curators

Axiom
annotated source: vascular bundle
annotated property: has_exact_synonym
annotated target: haz vascular (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vascular bundle
annotated property: has_exact_synonym
annotated target: 維管束 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

root primordium
type: Class
subclass of: primordium
subclass of: anatomical entity
subclass of: Restriction
  on property: develops_from
  some values from: root anlagen
definition: A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
has db xref: PO_GIT:467
has_exact_synonym: portion of root primordium tissue (exact)
has_exact_synonym: primordio de ra&#237z (Spanish, exact)
has_exact_synonym: root primordia (exact, plural)
has_exact_synonym: 根原基（可視的） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0005029
comment: A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

Axiom
annotated source: root primordium
annotated property: definition
annotated target: A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).
has db xref: ISBN:0521288959
has db xref: POC:curators

Axiom
annotated source: root primordium
annotated property: has_exact_synonym
annotated target: primordio de ra&#237z (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: root primordium
annotated property: has_exact_synonym
annotated target: root primordia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: root primordium
annotated property: has_exact_synonym
annotated target: 根原基（可視的） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

parenchyma
type: Class
subclass of: portion of ground tissue
definition: A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.
has db xref: PO_GIT:107
has_exact_synonym: par&#233nquima (Spanish, exact)
has_exact_synonym: portion of parenchyma tissue (exact)
has_exact_synonym: portion of parenchymatous tissue (exact)
has_exact_synonym: 柔組織 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0005421
in subset: TraitNet
comment: Parenchyma contains relatively unspecialized cells.

Axiom
annotated source: parenchyma
annotated property: definition
annotated target: A portion of ground tissue (PO:0025059) composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate, living protoplasts.
has db xref: POC:curators

Axiom
annotated source: parenchyma
annotated property: has_exact_synonym
annotated target: par&#233nquima (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: parenchyma
annotated property: has_exact_synonym
annotated target: 柔組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

cambium
type: Class
subclass of: lateral meristem
definition: A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.
has db xref: PO_GIT:437
has_exact_synonym: cambium (Spanish, exact)
has_exact_synonym: 形成層 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0005597
in subset: TraitNet
comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).

Axiom
annotated source: cambium
annotated property: definition
annotated target: A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.
has db xref: ISBN:047125208

Axiom
annotated source: cambium
annotated property: has_exact_synonym
annotated target: cambium (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: cambium
annotated property: has_exact_synonym
annotated target: 形成層 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

portion of secretory tissue
type: Class
subclass of: portion of plant tissue
definition: A portion of plant tissue (PO:0009007) that form specialized structures producing a secretion.
has db xref: PO_GIT:659
has_exact_synonym: porci&#243n del tejido secretor (Spanish, exact)
has_exact_synonym: 分泌組織の一部 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: gland (related)
id: PO:0005656
in subset: TraitNet
comment: The synonym gland does not imply non-secretory 'glands'.

Axiom
annotated source: portion of secretory tissue
annotated property: definition
annotated target: A portion of plant tissue (PO:0009007) that form specialized structures producing a secretion.
has db xref: Gramene:Pankaj_Jaiswal
has db xref: ISBN:0471245208
has db xref: POC:Laurel_Cooper

Axiom
annotated source: portion of secretory tissue
annotated property: has_exact_synonym
annotated target: porci&#243n del tejido secretor (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: portion of secretory tissue
annotated property: has_exact_synonym
annotated target: 分泌組織の一部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant epidermis
type: Class
subclass of: portion of plant tissue
subclass of: anatomical entity
subclass of: Restriction
  on property: develops_from
  some values from: protoderm
definition: A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011).
has db xref: PO_GIT:109
has_exact_synonym: dermal tissue (exact)
has_exact_synonym: epidermal layer (exact)
has_exact_synonym: epidermides (exact, plural)
has_exact_synonym: epidermis (Spanish, exact)
has_exact_synonym: epidermises (exact, plural)
has_exact_synonym: portion of epidermal tissue (exact)
has_exact_synonym: 表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: multiseriate epidermis (related)
id: PO:0005679
in subset: TraitNet
comment: The epidermis can be composed of one or more layers of cells. In some species of vascular plants, the epidermis, which is a primary tissue, is replaced by periderm, which is secondary tissue, later in development. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids.

Axiom
annotated source: plant epidermis
annotated property: definition
annotated target: A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011).
has db xref: POC:curators

Axiom
annotated source: plant epidermis
annotated property: has_exact_synonym
annotated target: epidermides (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: plant epidermis
annotated property: has_exact_synonym
annotated target: epidermis (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant epidermis
annotated property: has_exact_synonym
annotated target: epidermises (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: plant epidermis
annotated property: has_exact_synonym
annotated target: 表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome
type: Class
subclass of: plant organ
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: shoot system
subclass of: Restriction
  on property: develops_from
  some values from: phyllome primordium
definition: A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
has_exact_synonym: filoma (Spanish, exact)
has_exact_synonym: フィロム、葉(的）器官 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0006001
in subset: TraitNet
in subset: reference

Axiom
annotated source: phyllome
annotated property: definition
annotated target: A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148).
has db xref: POC:curators

Axiom
annotated source: phyllome
annotated property: has_exact_synonym
annotated target: filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome
annotated property: has_exact_synonym
annotated target: フィロム、葉(的）器官 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

scale leaf
type: Class
subclass of: phyllome
definition: A phyllome that is reduced in size relative to a vascular leaf on the same plant and is often associated with a perennating or dormant bud or a vegetatively propagating organ such as a rhizome.
has db xref: PO_GIT:273
has_exact_synonym: cat&#225fila en escama (Spanish, exact)
has_exact_synonym: 鱗片葉 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: cataphyll (related)
id: PO:0006003
in subset: TraitNet
in subset: reference
comment: May be photosynthetic or non-photosynthetic. Some species have vascular leaves that are scale-like (such as Juniperus, Thuja, and Chamaecyparis). Annotations for scale-like leaves should go under vascular leaf (PO:0009025), not scale leaf.

Axiom
annotated source: scale leaf
annotated property: definition
annotated target: A phyllome that is reduced in size relative to a vascular leaf on the same plant and is often associated with a perennating or dormant bud or a vegetatively propagating organ such as a rhizome.
has db xref: ISBN:0080374913

Axiom
annotated source: scale leaf
annotated property: has_exact_synonym
annotated target: cat&#225fila en escama (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: scale leaf
annotated property: has_exact_synonym
annotated target: 鱗片葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf epidermis
type: Class
equivalent class: Class
  intersection of: phyllome epidermis
  intersection of: Restriction
    on property: part of
    some values from: leaf
subclass of: phyllome epidermis
subclass of: Restriction
  on property: part of
  some values from: leaf
definition: A portion of phyllome epidermis (PO:0025157) that is part of a leaf (PO:0025034).
has_exact_synonym: epidermis de la hoja (Spanish, exact)
has_exact_synonym: foliage leaf epidermis (exact)
has_exact_synonym: phyllid epidermis (exact)
has_exact_synonym: 葉表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0006016
comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: leaf epidermis
annotated property: definition
annotated target: A portion of phyllome epidermis (PO:0025157) that is part of a leaf (PO:0025034).
has db xref: POC:curators

Axiom
annotated source: leaf epidermis
annotated property: has_exact_synonym
annotated target: epidermis de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf epidermis
annotated property: has_exact_synonym
annotated target: 葉表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf adaxial epidermis
type: Class
subclass of: leaf epidermis
definition: A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf (PO:0025034).
definition: A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf.
has_exact_synonym: epidermis adaxial de la hoja (Spanish, exact)
has_exact_synonym: 葉向軸側表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: upper epidermis (related)
has_related_synonym: upper leaf
id: PO:0006018
comment: Used to refer to an adaxial epidermis of an entire leaf. More specific terms exist for leaf lamina adaxial epidermis and petiole adaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
label: adaxial leaf epidermis

Axiom
annotated source: leaf adaxial epidermis
annotated property: definition
annotated target: A portion of leaf epidermis (PO:0006016) that covers the adaxial/upper surface of a leaf (PO:0025034).
has db xref: POC:Ramona_Walls

Axiom
annotated source: leaf adaxial epidermis
annotated property: has_exact_synonym
annotated target: epidermis adaxial de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf adaxial epidermis
annotated property: has_exact_synonym
annotated target: 葉向軸側表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf abaxial epidermis
type: Class
subclass of: leaf epidermis
definition: A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf (PO:0025034).
definition: A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf.
has_exact_synonym: epidermis abaxial de la hoja (Spanish, exact)
has_exact_synonym: leaf underside
has_exact_synonym: 葉背軸側表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: lower epidermis (related)
has_related_synonym: lower leaf
id: PO:0006019
comment: Used to refer to an abaxial epidermis of an entire leaf. More specific terms exist for leaf lamina abaxial epidermis and petiole abaxial epidermis. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
label: abaxial leaf epidermis

Axiom
annotated source: leaf abaxial epidermis
annotated property: definition
annotated target: A portion of leaf epidermis (PO:0006016) that covers the abaxial/lower surface of a leaf (PO:0025034).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: leaf abaxial epidermis
annotated property: has_exact_synonym
annotated target: epidermis abaxial de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf abaxial epidermis
annotated property: has_exact_synonym
annotated target: 葉背軸側表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot system epidermis
type: Class
equivalent class: Class
  intersection of: plant epidermis
  intersection of: Restriction
    on property: part of
    some values from: shoot system
subclass of: plant epidermis
subclass of: Restriction
  on property: part of
  some values from: shoot system
subclass of: Restriction
  on property: develops_from
  some values from: meristem L1 layer
definition: A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020).
has db xref: PO_GIT:111
has_exact_synonym: epidermis del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0006035
comment: Often interrupted by stomatal complexes (PO:0002000) and other structures. The shoot system epidermis is different from the root epidermis (PO:0006036) in its origin, function and structure.

Axiom
annotated source: shoot system epidermis
annotated property: definition
annotated target: A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020).
has db xref: ISBN:0471245208
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: shoot system epidermis
annotated property: has_exact_synonym
annotated target: epidermis del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot system epidermis
annotated property: has_exact_synonym
annotated target: シュート表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

root epidermis
type: Class
equivalent class: Class
  intersection of: plant epidermis
  intersection of: Restriction
    on property: part of
    some values from: root
subclass of: plant epidermis
subclass of: Restriction
  on property: part of
  some values from: root
definition: A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005).
has alternative id: PO:0006037
has db xref: PO_GIT:111
has_exact_synonym: epidermis de la ra&#237z (Spanish, exact)
has_exact_synonym: 根表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: epiblem (related)
has_related_synonym: rhizodermis (related)
id: PO:0006036
comment: The root epidermis is different from the shoot epidermis in its origin, function and structure.

Axiom
annotated source: root epidermis
annotated property: definition
annotated target: A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005).
has db xref: ISBN:0080374913

Axiom
annotated source: root epidermis
annotated property: has_exact_synonym
annotated target: epidermis de la ra&#237z (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: root epidermis
annotated property: has_exact_synonym
annotated target: 根表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot system meristem
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: part of
  some values from: shoot system
definition: A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
has db xref: PO_GIT:472
has db xref: PO_GIT:583
has_exact_synonym: meristema del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0006079
in subset: TraitNet

Axiom
annotated source: shoot system meristem
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
has db xref: Gramene:Pankaj_Jaiswal
has db xref: POC:Laurel_Cooper

Axiom
annotated source: shoot system meristem
annotated property: has_exact_synonym
annotated target: meristema del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot system meristem
annotated property: has_exact_synonym
annotated target: シュート分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

protoderm
type: Class
subclass of: portion of meristem tissue
definition: A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
has db xref: PO_GIT:125
has_exact_synonym: portion of protoderm tissue (exact)
has_exact_synonym: protodermis (Spanish, exact)
has_exact_synonym: 前表皮、原表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: dermatogen cell (related)
id: PO:0006210
comment: A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state.

Axiom
annotated source: protoderm
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679).
has db xref: ISBN:0471245208
has db xref: POC:Laurel_Cooper

Axiom
annotated source: protoderm
annotated property: has_exact_synonym
annotated target: protodermis (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: protoderm
annotated property: has_exact_synonym
annotated target: 前表皮、原表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf trichome
type: Class
subclass of: phyllome trichome
subclass of: Restriction
  on property: part of
  some values from: leaf epidermis
definition: A phyllome trichome that is part of a leaf epidermis.
has db xref: PO_GIT:232
has_exact_synonym: tricoma de hoja (Spanish, exact)
has_exact_synonym: 葉毛（毛茸、糸状体） (Japanese, exact)
has narrow synonym: phyllid trichome (narrow)
has OBO namespace: plant_anatomy
id: PO:0006504
in subset: TraitNet
comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: leaf trichome
annotated property: definition
annotated target: A phyllome trichome that is part of a leaf epidermis.
has db xref: POC:Ramona_Walls

Axiom
annotated source: leaf trichome
annotated property: has_exact_synonym
annotated target: tricoma de hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf trichome
annotated property: has_exact_synonym
annotated target: 葉毛（毛茸、糸状体） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

whole plant development stage
type: Class
subclass of: plant structure development stage
subclass of: Restriction
  on property: has participant
  some values from: whole plant
definition: A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
has db xref: PO_GIT:390
has OBO namespace: plant_structure_development_stage
has_related_synonym: Solanaceae whole plant growth stages (SGN:0000001) (related)
has_related_synonym: cereal plant growth stage ontology (GRO:0007199) (related)
has_related_synonym: maize growth stage (GRO:0007002) (related)
has_related_synonym: plant growth stages in Arabidopsis (TAIR:0000021) (related)
has_related_synonym: rice growth stage (GRO:0007040) (related)
has_related_synonym: sorghum growth stage (GRO:0007124) (related)
has_related_synonym: wheat, barley and oat growth stage (GRO:0007156) (related)
id: PO:0007033
in subset: TraitNet

Axiom
annotated source: whole plant development stage
annotated property: definition
annotated target: A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003).
has db xref: POC:curators

vegetative shoot apical meristem
type: Class
subclass of: shoot apical meristem
definition: A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs.
has db xref: PO_GIT:36
has_exact_synonym: meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: 栄養シュート頂端分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: vegetative meristem (related)
id: PO:0008016

Axiom
annotated source: vegetative shoot apical meristem
annotated property: definition
annotated target: A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs.
has db xref: Gramene:Chih-Wei_Tung

Axiom
annotated source: vegetative shoot apical meristem
annotated property: has_exact_synonym
annotated target: meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vegetative shoot apical meristem
annotated property: has_exact_synonym
annotated target: 栄養シュート頂端分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

reproductive shoot apical meristem
type: Class
subclass of: shoot apical meristem
subclass of: Restriction
  on property: part of
  some values from: reproductive shoot apex
definition: A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
has db xref: PO_GIT:36
has_exact_synonym: meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: 生殖シュート頂端 分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0008028

Axiom
annotated source: reproductive shoot apical meristem
annotated property: definition
annotated target: A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs.
has db xref: Gramene:Chih-Wei_Tung

Axiom
annotated source: reproductive shoot apical meristem
annotated property: has_exact_synonym
annotated target: meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: reproductive shoot apical meristem
annotated property: has_exact_synonym
annotated target: 生殖シュート頂端 分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

stem base
type: Class
subclass of: cardinal organ part
subclass of: Restriction
  on property: part of
  some values from: stem
definition: The basal part of stem.
has_exact_synonym: base del tallo (Spanish, exact)
has_exact_synonym: gametophore stem base (exact)
has_exact_synonym: 茎基部 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0008039

Axiom
annotated source: stem base
annotated property: definition
annotated target: The basal part of stem.
has db xref: Gramene:Chih-Wei_Tung

Axiom
annotated source: stem base
annotated property: has_exact_synonym
annotated target: base del tallo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem base
annotated property: has_exact_synonym
annotated target: 茎基部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

fruit
type: Class
subclass of: multi-tissue plant structure
subclass of: anatomical entity
subclass of: Restriction
  on property: develops_from
  some values from: gynoecium
definition: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
has alternative id: PO:0020067
has alternative id: PO:0020068
has alternative id: PO:0020069
has alternative id: PO:0020070
has alternative id: PO:0020071
has alternative id: PO:0020072
has alternative id: PO:0020073
has alternative id: PO:0020074
has alternative id: PO:0020076
has alternative id: PO:0020077
has alternative id: PO:0020078
has alternative id: PO:0020079
has alternative id: PO:0020080
has alternative id: PO:0020082
has alternative id: PO:0020083
has alternative id: PO:0020087
has alternative id: PO:0020107
has broad synonym: aggregate fruit (broad)
has broad synonym: compound fruit (broad)
has broad synonym: dehiscent fruit (broad)
has broad synonym: diaspore (broad)
has broad synonym: indehiscent fruit (broad)
has broad synonym: multiple fruit (broad)
has broad synonym: propagule (broad)
has db xref: PO_GIT:76
has_exact_synonym: frucht (exact, German)
has_exact_synonym: fruto (exact, Spanish)
has_exact_synonym: 果実 (exact, Japanese)
has narrow synonym: coenocarp (narrow)
has narrow synonym: syncarp (narrow)
has OBO namespace: plant_anatomy
id: PO:0009001
in subset: Angiosperm
in subset: Arabidopsis
in subset: Maize
in subset: Poaceae
in subset: Rice
in subset: TraitNet
comment: A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.

Axiom
annotated source: fruit
annotated property: definition
annotated target: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010).
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: fruit
annotated property: has_exact_synonym
annotated target: frucht (exact, German)
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has synonym type: German

Axiom
annotated source: fruit
annotated property: has_exact_synonym
annotated target: fruto (exact, Spanish)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: fruit
annotated property: has_exact_synonym
annotated target: 果実 (exact, Japanese)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: fruit
annotated property: hasNarrowSynonym
annotated target: coenocarp (narrow)

Axiom
annotated source: fruit
annotated property: hasNarrowSynonym
annotated target: syncarp (narrow)

plant cell
type: Class
subclass of: plant structure
disjoint with: portion of plant tissue
disjoint with: plant organ
disjoint with: cardinal organ part
disjoint with: collective plant organ structure
definition: A cell which is a plant structure (PO:0009011).
has broad synonym: cell (broad)
has db xref: GO:0005623
has db xref: PO_GIT:56
has_exact_synonym: c&#233lula vegetal (Spanish, exact)
has_exact_synonym: 植物細胞 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0009002
in subset: CL
in subset: TraitNet
in subset: reference
comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.

Axiom
annotated source: plant cell
annotated property: definition
annotated target: A cell which is a plant structure (PO:0009011).
has db xref: CL:0000000
has db xref: POC:curators

Axiom
annotated source: plant cell
annotated property: has_exact_synonym
annotated target: c&#233lula vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant cell
annotated property: has_exact_synonym
annotated target: 植物細胞 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

root
type: Class
subclass of: plant axis
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: root system
subclass of: Restriction
  on property: develops_from
  some values from: root primordium
definition: A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
has alternative id: PO:0003006
has db xref: PO_GIT:578
has_exact_synonym: ra&#237z (Spanish, exact)
has_exact_synonym: radices (exact, plural)
has_exact_synonym: radix (exact)
has_exact_synonym: 根 (Japanese, exact)
has narrow synonym: aerial root (narrow)
has narrow synonym: climbing root (narrow)
has OBO namespace: plant_anatomy
id: PO:0009005
in subset: Angiosperm
in subset: Gymnosperms
in subset: Maize
in subset: Musa
in subset: Potato
in subset: Rice
in subset: Tomato
in subset: TraitNet
in subset: reference
comment: Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034).

Axiom
annotated source: root
annotated property: definition
annotated target: A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately.
has db xref: ISBN:978-0879015329
has db xref: ISBN:9780964022157
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: root
annotated property: has_exact_synonym
annotated target: ra&#237z (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: root
annotated property: has_exact_synonym
annotated target: radices (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: root
annotated property: has_exact_synonym
annotated target: radix (exact)

Axiom
annotated source: root
annotated property: has_exact_synonym
annotated target: 根 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: root
annotated property: hasNarrowSynonym
annotated target: climbing root (narrow)

shoot system
type: Class
subclass of: collective plant organ structure
disjoint with: root system
definition: A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
has db xref: PO_GIT:135
has_exact_synonym: sistema de epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート系、苗条系 (Japanese, exact)
has narrow synonym: tree crown (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: Poaceae crown (related)
has_related_synonym: shoot (related)
has_related_synonym: thalli (related, plural)
has_related_synonym: thallus (related)
id: PO:0009006
in subset: TraitNet
in subset: reference
comment: The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system.

Axiom
annotated source: shoot system
annotated property: definition
annotated target: A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them.
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: shoot system
annotated property: has_exact_synonym
annotated target: sistema de epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot system
annotated property: has_exact_synonym
annotated target: シュート系、苗条系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: shoot system
annotated property: has_related_synonym
annotated target: thalli (related, plural)
has synonym type: OMO_0003004

Axiom
annotated source: shoot system
annotated property: has_related_synonym
annotated target: thallus (related)

portion of plant tissue
type: Class
subclass of: plant structure
disjoint with: plant organ
disjoint with: cardinal organ part
disjoint with: collective plant organ structure
definition: A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
has broad synonym: portion of tissue (broad)
has broad synonym: tissue (broad)
has db xref: PO_GIT:59
has_exact_synonym: porci&#243n de un tejido vegetal (Spanish, exact)
has_exact_synonym: 植物組織の一部 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: plant tissue (related)
id: PO:0009007
in subset: TraitNet
in subset: reference
comment: A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts.

Axiom
annotated source: portion of plant tissue
annotated property: definition
annotated target: A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.
has db xref: POC:curators
has db xref: TAIR_curator:Leonore_Reiser

Axiom
annotated source: portion of plant tissue
annotated property: has_exact_synonym
annotated target: porci&#243n de un tejido vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: portion of plant tissue
annotated property: has_exact_synonym
annotated target: 植物組織の一部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant organ
type: Class
subclass of: multi-tissue plant structure
definition: A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
has broad synonym: organ (broad)
has db xref: PATO:01503
has db xref: PO_GIT:55
has_exact_synonym: &#243rgano vegetal (Spanish, exact)
has_exact_synonym: 植物 器官 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: compound plant organ (related)
has_related_synonym: simple plant organ (related)
id: PO:0009008
in subset: TraitNet
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003).

Axiom
annotated source: plant organ
annotated property: definition
annotated target: A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
has db xref: POC:curators

Axiom
annotated source: plant organ
annotated property: has_exact_synonym
annotated target: &#243rgano vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant organ
annotated property: has_exact_synonym
annotated target: 植物 器官 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: plant organ
annotated property: has_related_synonym
annotated target: simple plant organ (related)
has db xref: PATO:01503

plant structure
type: Class
subclass of: plant anatomical entity
definition: A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
has db xref: PO_GIT:57
has_exact_synonym: estructura vegetal (Spanish, exact)
has_exact_synonym: 植物 構造 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0009011
in subset: TraitNet
comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome.
comment: These terms (i.e., subclasses of plant structure) can be used to describe the location of a plant gall (e.g., on leaf or stem) and also the parts of a gall (e.g., nectary, larval chamber).

Axiom
annotated source: plant structure
annotated property: definition
annotated target: A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant.
has db xref: CARO:0000003
has db xref: PO:cooperl
has db xref: POC:curators

Axiom
annotated source: plant structure
annotated property: has_exact_synonym
annotated target: estructura vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant structure
annotated property: has_exact_synonym
annotated target: 植物 構造 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: plant structure
annotated property: comment
annotated target: These terms (i.e., subclasses of plant structure) can be used to describe the location of a plant gall (e.g., on leaf or stem) and also the parts of a gall (e.g., nectary, larval chamber).
contributor: https://orcid.org/0000-0002-2119-4663

plant structure development stage
type: Class
subclass of: process
definition: A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
has alternative id: PO:0007021
has db xref: PO_GIT:185
has db xref: TAIR:0000205
has_exact_synonym: etapa de desarrollo de estructura vegetal (Spanish, exact)
has_exact_synonym: plant growth and development stage (exact)
has OBO namespace: plant_structure_development_stage
has_related_synonym: Arabidopsis growth (related)
id: PO:0009012
in subset: TraitNet
comment: Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'.

Axiom
annotated source: plant structure development stage
annotated property: definition
annotated target: A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
has db xref: BFO:0000003
has db xref: GO:0032502
has db xref: POC:curators

Axiom
annotated source: plant structure development stage
annotated property: has_exact_synonym
annotated target: etapa de desarrollo de estructura vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant structure development stage
annotated property: has_related_synonym
annotated target: Arabidopsis growth (related)
has db xref: TAIR:0000205

portion of meristem tissue
type: Class
subclass of: portion of plant tissue
subclass of: Restriction
  on property: has part
  some values from: meristematic cell
definition: A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
has db xref: PO_GIT:472
has_exact_synonym: meristem (exact)
has_exact_synonym: meristema (Spanish, exact)
has_exact_synonym: meristematic tissue (exact)
has_exact_synonym: 分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0009013
in subset: TraitNet

Axiom
annotated source: portion of meristem tissue
annotated property: definition
annotated target: A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth.
has db xref: APweb:Glossary
has db xref: Gramene:Pankaj_Jaiswal

Axiom
annotated source: portion of meristem tissue
annotated property: has_exact_synonym
annotated target: meristema (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: portion of meristem tissue
annotated property: has_exact_synonym
annotated target: 分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

portion of vascular tissue
type: Class
subclass of: portion of plant tissue
definition: A portion of plant tissue (PO:0009007) that has as part one or more tracheary elements (PO:0000290) or sieve elements (PO:0025406).
has db xref: BTO:0001432
has db xref: PO_GIT:431
has_exact_synonym: porci&#243n de tejido vascular (Spanish, exact)
has_exact_synonym: vascular tissue (exact)
has_exact_synonym: 維管束細胞の一部 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: vascular system (related)
id: PO:0009015
in subset: TraitNet
comment: Functions in conduction and support. In shoot axes (PO:0025029), vascular tissue is often found as part of a shoot axis stele (PO:0025198) or as scattered vascular bundles (PO:0005020). May include other types of tissues or cells, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).

Axiom
annotated source: portion of vascular tissue
annotated property: definition
annotated target: A portion of plant tissue (PO:0009007) that has as part one or more tracheary elements (PO:0000290) or sieve elements (PO:0025406).
has db xref: POC:curators

Axiom
annotated source: portion of vascular tissue
annotated property: has_exact_synonym
annotated target: porci&#243n de tejido vascular (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: portion of vascular tissue
annotated property: has_exact_synonym
annotated target: 維管束細胞の一部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

meristem L1 layer
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: part of
  some values from: shoot apical meristem
definition: A portion of meristem tissue (PO:0009013) that is the outermost layer of a shoot apical meristem (PO:0020148) and gives rise to a shoot system epidermis (PO:0006035).
has db xref: PO_GIT:150
has db xref: PO_GIT:576
has_exact_synonym: meristema L1 (Spanish, exact)
has_exact_synonym: 分裂組織 L1 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: tunica (related)
id: PO:0009020
comment: The cells of the meristem L1 layer divide in a strictly anticlinical fashion.

Axiom
annotated source: meristem L1 layer
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that is the outermost layer of a shoot apical meristem (PO:0020148) and gives rise to a shoot system epidermis (PO:0006035).
has db xref: Gramene:Pankaj_Jaiswal
has db xref: PMID:11283725
has db xref: PMID:12221985
has db xref: POC:Laurel_Cooper

Axiom
annotated source: meristem L1 layer
annotated property: has_exact_synonym
annotated target: meristema L1 (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: meristem L1 layer
annotated property: has_exact_synonym
annotated target: 分裂組織 L1 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf axil
type: Class
subclass of: axil
definition: An axil that is the space between a shoot axis and a leaf that branches from the shoot axis.
has db xref: PO_GIT:104
has_exact_synonym: hoja axilar (Spanish, exact)
has_exact_synonym: 葉軸 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0009023

Axiom
annotated source: leaf axil
annotated property: definition
annotated target: An axil that is the space between a shoot axis and a leaf that branches from the shoot axis.
has db xref: POC:Ramona_Walls

Axiom
annotated source: leaf axil
annotated property: has_exact_synonym
annotated target: hoja axilar (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf axil
annotated property: has_exact_synonym
annotated target: 葉軸 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

vascular leaf
type: Class
subclass of: leaf
subclass of: Restriction
  on property: participates in
  some values from: sporophyte development stage
subclass of: Restriction
  on property: develops_from
  some values from: vascular leaf primordium
definition: A leaf (PO:0025034) in a vascular plant.
has db xref: PO_GIT:137
has_exact_synonym: foliage leaf (exact)
has_exact_synonym: hoja vascular (Spanish, exact)
has_exact_synonym: leaf, vascular (exact)
has_exact_synonym: vascular leaves (exact, plural)
has_exact_synonym: 維管束のある葉, または維管束植物の葉 (Japanese, exact)
has narrow synonym: ascidia (narrow)
has narrow synonym: ascidium (narrow)
has narrow synonym: fiddlehead (narrow)
has narrow synonym: frond (narrow)
has narrow synonym: needle-like leaf (narrow)
has narrow synonym: pitcher (narrow)
has narrow synonym: pitcher blade (narrow)
has narrow synonym: pitcher-blade (narrow)
has narrow synonym: scale-like leaf (narrow)
has narrow synonym: sterile frond (narrow)
has narrow synonym: trophophyll (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: crozier (related)
has_related_synonym: macrophyll (related)
has_related_synonym: megaphyll (related)
id: PO:0009025
in subset: Angiosperm
in subset: Arabidopsis
in subset: Citrus
in subset: Gymnosperms
in subset: Maize
in subset: Musa
in subset: Potato
in subset: Pteridophytes
in subset: Rice
in subset: Tomato
in subset: TraitNet
in subset: reference
comment: Has vascular tissue. From APweb Glossary: In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud. Occurs in the sporophytic phase of a plant life cycle.

Axiom
annotated source: vascular leaf
annotated property: definition
annotated target: A leaf (PO:0025034) in a vascular plant.
has db xref: POC:curators

Axiom
annotated source: vascular leaf
annotated property: has_exact_synonym
annotated target: hoja vascular (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vascular leaf
annotated property: has_exact_synonym
annotated target: vascular leaves (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: vascular leaf
annotated property: has_exact_synonym
annotated target: 維管束のある葉, または維管束植物の葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: ascidia (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: ascidium (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: fiddlehead (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: pitcher (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: pitcher blade (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: pitcher-blade (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: sterile frond (narrow)

Axiom
annotated source: vascular leaf
annotated property: hasNarrowSynonym
annotated target: trophophyll (narrow)

Axiom
annotated source: vascular leaf
annotated property: has_related_synonym
annotated target: crozier (related)

Axiom
annotated source: vascular leaf
annotated property: has_related_synonym
annotated target: macrophyll (related)

Axiom
annotated source: vascular leaf
annotated property: has_related_synonym
annotated target: megaphyll (related)

nectary
type: Class
subclass of: portion of secretory tissue
subclass of: Restriction
  on property: part of
  some values from: shoot system
definition: A portion of secretory tissue (PO:0005656) which is a multicellular glandular structure secreting a liquid containing organic substances, including sugars.
has db xref: PO_GIT:659
has_exact_synonym: nectario (Spanish, exact)
has_exact_synonym: 蜜腺 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0009035
in subset: TraitNet
in subset: reference

Axiom
annotated source: nectary
annotated property: definition
annotated target: A portion of secretory tissue (PO:0005656) which is a multicellular glandular structure secreting a liquid containing organic substances, including sugars.
has db xref: Gramene:Pankaj_Jaiswal
has db xref: ISBN:0471245208
has db xref: POC:Laurel_Cooper

Axiom
annotated source: nectary
annotated property: has_exact_synonym
annotated target: nectario (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: nectary
annotated property: has_exact_synonym
annotated target: 蜜腺 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

flower
type: Class
subclass of: reproductive shoot system
subclass of: anatomical entity
subclass of: Restriction
  on property: develops_from
  some values from: flower meristem
definition: A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
has alternative id: PO:0004541
has db xref: PO_GIT:160
has db xref: PO_GIT:259
has_exact_synonym: flor (Spanish, exact)
has_exact_synonym: 花 (Japanese, exact)
has narrow synonym: Asteraceae floret (narrow)
has narrow synonym: basal flower (narrow)
has narrow synonym: double flower (narrow)
has narrow synonym: hermaphrodite flower (narrow)
has narrow synonym: monoclinous flower (narrow)
has narrow synonym: perfect flower (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: floret (related)
id: PO:0009046
in subset: Angiosperm
in subset: TraitNet
in subset: reference
comment: The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form.

Axiom
annotated source: flower
annotated property: definition
annotated target: A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part.
has db xref: POC:curators

Axiom
annotated source: flower
annotated property: has_exact_synonym
annotated target: flor (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: flower
annotated property: has_exact_synonym
annotated target: 花 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: flower
annotated property: hasNarrowSynonym
annotated target: basal flower (narrow)
has db xref: CO_125:0000019

Axiom
annotated source: flower
annotated property: hasNarrowSynonym
annotated target: hermaphrodite flower (narrow)
has db xref: CO_125:0000028

stem
type: Class
subclass of: shoot axis
definition: A shoot axis (PO:0025029) that is the primary axis of a plant.
has db xref: PO_GIT:52
has db xref: PO_GIT:96
has_exact_synonym: ca&#241a (Spanish, exact)
has_exact_synonym: culm (exact)
has_exact_synonym: eje primario (Spanish, exact)
has_exact_synonym: primary axis (exact)
has_exact_synonym: primary stem (exact)
has_exact_synonym: tallo (Spanish, exact)
has_exact_synonym: tronco (Spanish, exact)
has_exact_synonym: 茎 (Japanese, exact)
has narrow synonym: bole (narrow)
has narrow synonym: cane (narrow)
has narrow synonym: caudex (narrow)
has narrow synonym: caudices (narrow, plural)
has narrow synonym: core (narrow)
has narrow synonym: primocane (narrow)
has narrow synonym: scape (narrow)
has narrow synonym: stalk (narrow)
has narrow synonym: trunk (narrow)
has OBO namespace: plant_anatomy
id: PO:0009047
in subset: TraitNet
in subset: reference
comment: A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic.

Axiom
annotated source: stem
annotated property: definition
annotated target: A shoot axis (PO:0025029) that is the primary axis of a plant.
has db xref: POC:curators

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: ca&#241a (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: eje primario (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: primary stem (exact)

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: tallo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: tronco (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem
annotated property: has_exact_synonym
annotated target: 茎 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: stem
annotated property: hasNarrowSynonym
annotated target: bole (narrow)

Axiom
annotated source: stem
annotated property: hasNarrowSynonym
annotated target: caudex (narrow)

Axiom
annotated source: stem
annotated property: hasNarrowSynonym
annotated target: caudices (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: stem
annotated property: hasNarrowSynonym
annotated target: primocane (narrow)

Axiom
annotated source: stem
annotated property: hasNarrowSynonym
annotated target: scape (narrow)

inflorescence
type: Class
subclass of: reproductive shoot system
subclass of: multi-tissue plant structure
subclass of: anatomical entity
subclass of: Restriction
  on property: has part
  some values from: flower
subclass of: Restriction
  on property: participates in
  some values from: inflorescence development stage
definition: A reproductive shoot system (PO:0025082) that has as parts all of the shoot axes (PO:0025029) and flowers (PO:0009046; must have two or more) distal to the most distal leaf (PO:0009025).
has alternative id: PO:0009048
has alternative id: PO:0009050
has alternative id: PO:0020088
has alternative id: PO:0020111
has alternative id: PO:0020112
has alternative id: PO:0020113
has alternative id: PO:0020114
has alternative id: PO:0020115
has alternative id: PO:0020116
has alternative id: PO:0020117
has alternative id: PO:0020118
has alternative id: PO:0020119
has alternative id: PO:0020120
has db xref: PO_GIT:260
has db xref: PO_GIT:71
has_exact_synonym: inflorescencia (Spanish, exact)
has_exact_synonym: 花序 (Japanese, exact)
has narrow synonym: Triticeae spike (narrow)
has OBO namespace: plant_anatomy
id: PO:0009049
in subset: Angiosperm
in subset: TraitNet
in subset: reference
comment: An inflorescence is a reproductive shoot system from which at least two flowers develop. The growth pattern of an inflorescence may be monopodial (single main shoot axis), sympodial (growth only occurs from axillary meristems), or both. An inflorescence axis (PO:0020122) can be determinate or indeterminate. An inflorescence flower pedicel (PO:0009052) is the ultimate axis in an inflorescence. The flower (PO:0009046) of many plants, for example Magnolia spp., is solitary.

Axiom
annotated source: inflorescence
annotated property: definition
annotated target: A reproductive shoot system (PO:0025082) that has as parts all of the shoot axes (PO:0025029) and flowers (PO:0009046; must have two or more) distal to the most distal leaf (PO:0009025).
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has db xref: POC:Laurel_Cooper
has db xref: POC:Ramona_Walls

Axiom
annotated source: inflorescence
annotated property: has_exact_synonym
annotated target: inflorescencia (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: inflorescence
annotated property: has_exact_synonym
annotated target: 花序 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

gynoecium
type: Class
subclass of: collective phyllome structure
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: flower
subclass of: Restriction
  on property: develops_from
  some values from: gynoecium primordium
definition: A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
has alternative id: PO:0006317
has alternative id: PO:0006357
has alternative id: PO:0006365
has alternative id: PO:0006384
has alternative id: PO:0006391
has alternative id: PO:0006394
has alternative id: PO:0006403
has alternative id: PO:0006404
has alternative id: PO:0006423
has alternative id: PO:0006424
has alternative id: PO:0006425
has alternative id: PO:0006426
has alternative id: PO:0025089
has broad synonym: pistil (broad)
has db xref: PO_GIT:470
has db xref: PO_GIT:71
has db xref: PO_GIT:98
has_exact_synonym: ginoecio (Spanish, exact)
has_exact_synonym: gynaecium (exact)
has_exact_synonym: gynoecia (exact, plural)
has_exact_synonym: 雌蕊群 (Japanese, exact)
has narrow synonym: Poaceae gynoecium (narrow)
has narrow synonym: Zea gynoecium (narrow)
has narrow synonym: apocarpous gynoecium (narrow)
has narrow synonym: gynoecium of ear floret (narrow)
has narrow synonym: gynoecium of lower floret of pedicellate spikelet of ear (narrow)
has narrow synonym: gynoecium of lower floret of pedicellate spikelet of tassel (narrow)
has narrow synonym: gynoecium of lower floret of sessile spikelet of ear (narrow)
has narrow synonym: gynoecium of lower floret of sessile spikelet of tassel (narrow)
has narrow synonym: gynoecium of tassel floret (narrow)
has narrow synonym: gynoecium of upper floret of pedicellate spikelet of ear (narrow)
has narrow synonym: gynoecium of upper floret of pedicellate spikelet of tassel (narrow)
has narrow synonym: gynoecium of upper floret of sessile spikelet of ear (narrow)
has narrow synonym: gynoecium of upper floret of sessile spikelet of tassel (narrow)
has narrow synonym: syncarpous gynoecium (narrow)
has OBO namespace: plant_anatomy
id: PO:0009062
in subset: TraitNet
in subset: reference
comment: If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).

Axiom
annotated source: gynoecium
annotated property: definition
annotated target: A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046).
has db xref: POC:curators

Axiom
annotated source: gynoecium
annotated property: has_exact_synonym
annotated target: ginoecio (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: gynoecium
annotated property: has_exact_synonym
annotated target: gynaecium (exact)

Axiom
annotated source: gynoecium
annotated property: has_exact_synonym
annotated target: gynoecia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: gynoecium
annotated property: has_exact_synonym
annotated target: 雌蕊群 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

petiole
type: Class
subclass of: stalk
subclass of: Restriction
  on property: part of
  some values from: vascular leaf
definition: A stalk (PO:0025066) of a vascular leaf (PO:0009025).
has_exact_synonym: pec&#237olo (Spanish, exact)
has_exact_synonym: 葉柄 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0020038
in subset: TraitNet

Axiom
annotated source: petiole
annotated property: definition
annotated target: A stalk (PO:0025066) of a vascular leaf (PO:0009025).
has db xref: APweb:Glossary
has db xref: Gramene:Pankaj_Jaiswal

Axiom
annotated source: petiole
annotated property: has_exact_synonym
annotated target: pec&#237olo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: petiole
annotated property: has_exact_synonym
annotated target: 葉柄 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf lamina
type: Class
subclass of: phyllome lamina
subclass of: Restriction
  on property: part of
  some values from: leaf
definition: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
has db xref: PO_GIT:428
has db xref: PO_GIT:70
has_exact_synonym: l&#225mina de la hoja (Spanish, exact)
has_exact_synonym: 葉身（葉片） (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: leaf blade (related)
id: PO:0020039
in subset: TraitNet
comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae. If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: leaf lamina
annotated property: definition
annotated target: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
has db xref: POC:curators

Axiom
annotated source: leaf lamina
annotated property: has_exact_synonym
annotated target: l&#225mina de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf lamina
annotated property: has_exact_synonym
annotated target: 葉身（葉片） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

compound leaf
type: Class
subclass of: vascular leaf
definition: A leaf having two or more distinct leaflets that are evident as such from early in development.
has_exact_synonym: hoja compuesta (Spanish, exact)
has_exact_synonym: 複葉 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0020043

Axiom
annotated source: compound leaf
annotated property: definition
annotated target: A leaf having two or more distinct leaflets that are evident as such from early in development.
has db xref: APweb:Glossary

Axiom
annotated source: compound leaf
annotated property: has_exact_synonym
annotated target: hoja compuesta (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: compound leaf
annotated property: has_exact_synonym
annotated target: 複葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaflet
type: Class
subclass of: cardinal organ part
subclass of: Restriction
  on property: part of
  some values from: compound leaf
definition: A cardinal organ part (PO:0025001) that is one of the ultimate segments of a compound leaf (PO:0020043).
has db xref: PO_GIT:70
has_exact_synonym: fol&#237olo (Spanish, exact)
has_exact_synonym: 小葉 (Japanese, exact)
has narrow synonym: pinna (narrow)
has narrow synonym: pinnae (narrow, plural)
has narrow synonym: pinnule (narrow)
has OBO namespace: plant_anatomy
id: PO:0020049
in subset: TraitNet

Axiom
annotated source: leaflet
annotated property: definition
annotated target: A cardinal organ part (PO:0025001) that is one of the ultimate segments of a compound leaf (PO:0020043).
has db xref: APweb:Glossary
has db xref: POC:laurel_cooper

Axiom
annotated source: leaflet
annotated property: has_exact_synonym
annotated target: fol&#237olo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaflet
annotated property: has_exact_synonym
annotated target: 小葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: leaflet
annotated property: hasNarrowSynonym
annotated target: pinna (narrow)

Axiom
annotated source: leaflet
annotated property: hasNarrowSynonym
annotated target: pinnae (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: leaflet
annotated property: hasNarrowSynonym
annotated target: pinnule (narrow)

bud scale leaf
type: Class
subclass of: scale leaf
definition: A scale leaf that surrounds a dormant or perennating bud.
has_exact_synonym: bud scale (exact)
has_exact_synonym: escama de la yema (Spanish, exact)
has_exact_synonym: 芽鱗片葉 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0020054

Axiom
annotated source: bud scale leaf
annotated property: definition
annotated target: A scale leaf that surrounds a dormant or perennating bud.
has db xref: UMSL_curator:tk

Axiom
annotated source: bud scale leaf
annotated property: has_exact_synonym
annotated target: escama de la yema (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: bud scale leaf
annotated property: has_exact_synonym
annotated target: 芽鱗片葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf margin
type: Class
equivalent class: Class
  intersection of: phyllome margin
  intersection of: Restriction
    on property: part of
    some values from: leaf
subclass of: phyllome margin
subclass of: Restriction
  on property: part of
  some values from: leaf
definition: A phyllome margin (PO:0025018) that is part of a leaf (PO:0025034).
has db xref: PO_GIT:85
has_exact_synonym: margen de la hoja (Spanish, exact)
has_exact_synonym: 葉縁 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0020128
in subset: TraitNet
comment: If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.

Axiom
annotated source: leaf margin
annotated property: definition
annotated target: A phyllome margin (PO:0025018) that is part of a leaf (PO:0025034).
has db xref: POC:curators

Axiom
annotated source: leaf margin
annotated property: has_exact_synonym
annotated target: margen de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf margin
annotated property: has_exact_synonym
annotated target: 葉縁 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf lamina vein
type: Class
subclass of: phyllome lamina vein
subclass of: Restriction
  on property: part of
  some values from: leaf lamina vascular system
definition: A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048).
has db xref: PO_GIT:410
has db xref: PO_GIT:435
has_exact_synonym: leaf lamina vascular bundle (exact)
has_exact_synonym: leaf lamina vein
has_exact_synonym: vena de la hoja (Spanish, exact)
has_exact_synonym: 葉身葉脈 ？ (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0020138
in subset: TraitNet
label: leaf vein

Axiom
annotated source: leaf lamina vein
annotated property: definition
annotated target: A phyllome lamina vein (PO:0025348) that is part of a leaf lamina vascular system (PO:0000048).
has db xref: POC:curators

Axiom
annotated source: leaf lamina vein
annotated property: has_exact_synonym
annotated target: vena de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf lamina vein
annotated property: has_exact_synonym
annotated target: 葉身葉脈 ？ (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf midvein
type: Class
subclass of: primary leaf vein
definition: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
has broad synonym: mid rib (broad)
has broad synonym: mid-rib (broad)
has broad synonym: midrib (broad)
has db xref: PO_GIT:435
has_exact_synonym: vascular leaf midvein
has_exact_synonym: vascular leaf midvein (exact)
has_exact_synonym: vena media @es
has_exact_synonym: vena media (Spanish, exact)
has_exact_synonym: 葉主脈、中央脈、中脈 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: mid rib
has_related_synonym: mid-rib
has_related_synonym: midrib
has_related_synonym: vascular leaf costa (related)
has_related_synonym: vascular leaf costae (related, plural)
id: PO:0020139
comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).

Axiom
annotated source: leaf midvein
annotated property: definition
annotated target: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
has db xref: POC:curators

Axiom
annotated source: leaf midvein
annotated property: has_exact_synonym
annotated target: vena media (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf midvein
annotated property: has_exact_synonym
annotated target: 葉主脈、中央脈、中脈 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: leaf midvein
annotated property: has_related_synonym
annotated target: vascular leaf costa (related)

Axiom
annotated source: leaf midvein
annotated property: has_related_synonym
annotated target: vascular leaf costae (related, plural)
has synonym type: OMO_0003004

secondary leaf vein
type: Class
subclass of: leaf lamina vein
definition: A leaf lamina vein (PO:0020138) arising from a primary leaf vein (PO:0025413).
has db xref: PO_GIT:435
has_exact_synonym: vena secundaria (Spanish, exact)
has_exact_synonym: 二次葉脈 (Japanese, exact)
has narrow synonym: cross-vein (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: veinlet (related)
id: PO:0020140
comment: Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms.

Axiom
annotated source: secondary leaf vein
annotated property: definition
annotated target: A leaf lamina vein (PO:0020138) arising from a primary leaf vein (PO:0025413).
has db xref: Gramene:Pankaj_Jaiswal

Axiom
annotated source: secondary leaf vein
annotated property: has_exact_synonym
annotated target: vena secundaria (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: secondary leaf vein
annotated property: has_exact_synonym
annotated target: 二次葉脈 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: secondary leaf vein
annotated property: hasNarrowSynonym
annotated target: cross-vein (narrow)

apical meristem
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: has part
  some values from: protoderm
definition: A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
has broad synonym: promeristem (broad)
has db xref: PO_GIT:579
has_exact_synonym: AM (exact)
has_exact_synonym: meristema apical (Spanish, exact)
has_exact_synonym: 頂端分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: primary meristem (related)
id: PO:0020144
in subset: TraitNet

Axiom
annotated source: apical meristem
annotated property: definition
annotated target: A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025).
has db xref: Gramene:Pankaj_Jaiswal
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: apical meristem
annotated property: has_exact_synonym
annotated target: meristema apical (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: apical meristem
annotated property: has_exact_synonym
annotated target: 頂端分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

lateral meristem
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: part of
  some values from: plant axis
definition: A portion of meristem (PO:0009013) tissue located parallel to the sides of a shoot axis (PO:0025029) or root (PO:0009005) that participates in lateral growth.
has db xref: PO_GIT:437
has_exact_synonym: lateral growth meristem (exact)
has_exact_synonym: meristema lateral (Spanish, exact)
has_exact_synonym: 側 分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: secondary meristem (related)
id: PO:0020145
in subset: TraitNet
comment: A term for lateral growth has been requested in GO. Lateral meristems contribute to an increase in the cross-sectional area of a shoot axis or root. Examples of lateral meristems are: cambium (PO:0005597) (includes cork cambium (PO:0005599) and vascular cambium (PO:0005598)), shoot lateral meristem (PO:0006344) (includes primary thickening meristem (PO:0005039)), root lateral meristem (PO:0006308), and secondary thickening meristem (PO:0025414). Contrasts with apical meristem (PO:0020144), phyllome marginal meristem (PO:0025404), or intercalary meristem (PO:0006073).

Axiom
annotated source: lateral meristem
annotated property: definition
annotated target: A portion of meristem (PO:0009013) tissue located parallel to the sides of a shoot axis (PO:0025029) or root (PO:0009005) that participates in lateral growth.
has db xref: ISBN:047125208

Axiom
annotated source: lateral meristem
annotated property: has_exact_synonym
annotated target: meristema lateral (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: lateral meristem
annotated property: has_exact_synonym
annotated target: 側 分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot apical meristem
type: Class
subclass of: shoot system meristem
subclass of: apical meristem
subclass of: Restriction
  on property: part of
  some values from: shoot axis apex
definition: A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
has broad synonym: promeristem (broad)
has db xref: PO_GIT:472
has_exact_synonym: SAM (exact)
has_exact_synonym: meristema apical del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: 茎頂分裂組織 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: primary shoot meristem (related)
id: PO:0020148
in subset: TraitNet

Axiom
annotated source: shoot apical meristem
annotated property: definition
annotated target: A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
has db xref: POC:Laurel_Cooper
has db xref: UMSL_curator:fz

Axiom
annotated source: shoot apical meristem
annotated property: has_exact_synonym
annotated target: meristema apical del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot apical meristem
annotated property: has_exact_synonym
annotated target: 茎頂分裂組織 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

cardinal organ part
type: Class
equivalent class: Class
  intersection of: cardinal part of multi-tissue plant structure
  intersection of: Restriction
    on property: part of
    some values from: plant organ
subclass of: cardinal part of multi-tissue plant structure
subclass of: Restriction
  on property: part of
  some values from: plant organ
definition: A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
created by: rwalls
creation date: 2010-02-11T01:18:24Z
has db xref: PO_GIT:52
has db xref: PO_GIT:60
has_exact_synonym: cardinal part of plant organ (exact)
has_exact_synonym: parte de un &#243rgano cardinal (Spanish, exact)
has_exact_synonym: 基本的な（主要な）器官部 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025001
in subset: Arabidopsis
in subset: TraitNet
comment: Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.

Axiom
annotated source: cardinal organ part
annotated property: definition
annotated target: A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
has db xref: POC:curators

Axiom
annotated source: cardinal organ part
annotated property: has_exact_synonym
annotated target: parte de un &#243rgano cardinal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: cardinal organ part
annotated property: has_exact_synonym
annotated target: 基本的な（主要な）器官部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant axis
type: Class
subclass of: plant organ
definition: An axial plant organ (PO:0009008).
created by: rwalls
creation date: 2010-07-01T03:44:41Z
has_exact_synonym: eje de la planta (Spanish, exact)
has_exact_synonym: plant axes (exact, plural)
has_exact_synonym: 植物軸（軸柱） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025004
in subset: TraitNet
comment: Includes roots and shoots.

Axiom
annotated source: plant axis
annotated property: definition
annotated target: An axial plant organ (PO:0009008).
has db xref: POC:curators

Axiom
annotated source: plant axis
annotated property: has_exact_synonym
annotated target: eje de la planta (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant axis
annotated property: has_exact_synonym
annotated target: plant axes (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: plant axis
annotated property: has_exact_synonym
annotated target: 植物軸（軸柱） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant organ margin
type: Class
subclass of: cardinal organ part
subclass of: Restriction
  on property: part of
  some values from: plant organ lamina
definition: A cardinal organ part (PO:0025001) that is the edge of a plant organ (PO:0009008) and the area immediately internally adjacent to it.
created by: rwalls
creation date: 2010-03-12T10:33:57Z
has db xref: PO_GIT:52
has db xref: PO_GIT:70
has db xref: PO_GIT:72
has_exact_synonym: margen de un &#243rgano (Spanish, exact)
has_exact_synonym: 器官縁 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025005
in subset: TraitNet
comment: Only flattened or laminar plant organs or organ parts will have a margin.

Axiom
annotated source: plant organ margin
annotated property: definition
annotated target: A cardinal organ part (PO:0025001) that is the edge of a plant organ (PO:0009008) and the area immediately internally adjacent to it.
has db xref: POC:curators
has db xref: POC:laurel_cooper

Axiom
annotated source: plant organ margin
annotated property: has_exact_synonym
annotated target: margen de un &#243rgano (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant organ margin
annotated property: has_exact_synonym
annotated target: 器官縁 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

collective plant organ structure
type: Class
subclass of: collective plant structure
subclass of: Restriction
  on property: has part
  some values from: plant organ
definition: A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
created by: rwalls
creation date: 2010-02-09T04:12:11Z
has db xref: PO_GIT:63
has_exact_synonym: estructura vegetal colectiva de &#243rgano (Spanish, exact)
has_exact_synonym: 集合植物器官構造 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025007
in subset: TraitNet
comment: Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure.

Axiom
annotated source: collective plant organ structure
annotated property: definition
annotated target: A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).
has db xref: POC:curators

Axiom
annotated source: collective plant organ structure
annotated property: has_exact_synonym
annotated target: estructura vegetal colectiva de &#243rgano (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: collective plant organ structure
annotated property: has_exact_synonym
annotated target: 集合植物器官構造 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome margin
type: Class
equivalent class: Class
  intersection of: plant organ margin
  intersection of: Restriction
    on property: part of
    some values from: phyllome lamina
subclass of: plant organ margin
subclass of: Restriction
  on property: part of
  some values from: phyllome lamina
definition: A plant organ margin (PO:0025005) that is part of a phyllome lamina (PO:0025396).
created by: rwalls
creation date: 2010-04-02T10:51:16Z
has db xref: PO_GIT:70
has_exact_synonym: margen del filoma (Spanish, exact)
has_exact_synonym: フィロム縁 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025018
in subset: TraitNet

Axiom
annotated source: phyllome margin
annotated property: definition
annotated target: A plant organ margin (PO:0025005) that is part of a phyllome lamina (PO:0025396).
has db xref: POC:curators
has db xref: POC:laurel_cooper

Axiom
annotated source: phyllome margin
annotated property: has_exact_synonym
annotated target: margen del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome margin
annotated property: has_exact_synonym
annotated target: フィロム縁 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

collective phyllome structure
type: Class
subclass of: collective plant organ structure
definition: A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
created by: Laurel_Cooper
creation date: 2010-04-28T11:04:34Z
has alternative id: PO:0008033
has broad synonym: cycle (broad)
has broad synonym: verticil (broad)
has db xref: GO:0048438
has db xref: GO:0048457
has db xref: GO:0048458
has db xref: GO:0048459
has db xref: PO_GIT:90
has db xref: PO_GIT:99
has_exact_synonym: estructura colectiva del filoma (Spanish, exact)
has_exact_synonym: 葉的器官が集まった構造 (Japanese, exact)
has narrow synonym: floral whorl (narrow)
has narrow synonym: whorl (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: phyllome whorl (related)
id: PO:0025023
in subset: TraitNet

Axiom
annotated source: collective phyllome structure
annotated property: definition
annotated target: A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005).
has db xref: POC:curators

Axiom
annotated source: collective phyllome structure
annotated property: hasBroadSynonym
annotated target: cycle (broad)

Axiom
annotated source: collective phyllome structure
annotated property: hasBroadSynonym
annotated target: verticil (broad)

Axiom
annotated source: collective phyllome structure
annotated property: has_exact_synonym
annotated target: estructura colectiva del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: collective phyllome structure
annotated property: has_exact_synonym
annotated target: 葉的器官が集まった構造 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: collective phyllome structure
annotated property: hasNarrowSynonym
annotated target: floral whorl (narrow)
has db xref: GO:0048438
has db xref: GO:0048457
has db xref: GO:0048458
has db xref: GO:0048459

root system
type: Class
subclass of: collective plant organ structure
subclass of: Restriction
  on property: participates in
  some values from: sporophyte development stage
definition: A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
created by: rwalls
creation date: 2010-07-01T02:11:26Z
has broad synonym: root (broad)
has db xref: PO_GIT:136
has_exact_synonym: sistema de ra&#237z (Spanish, exact)
has_exact_synonym: 根系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025025
in subset: TraitNet
comment: Generally the below ground portion of a vascular plant.

Axiom
annotated source: root system
annotated property: definition
annotated target: A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof.
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: root system
annotated property: hasBroadSynonym
annotated target: root (broad)

Axiom
annotated source: root system
annotated property: has_exact_synonym
annotated target: sistema de ra&#237z (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: root system
annotated property: has_exact_synonym
annotated target: 根系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot axis
type: Class
subclass of: plant axis
subclass of: Restriction
  on property: part of
  some values from: shoot system
definition: A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
created by: rwalls
creation date: 2010-07-01T03:46:35Z
has_exact_synonym: caullome (exact)
has_exact_synonym: eje del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート軸 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: shoot (related)
id: PO:0025029
in subset: Angiosperm
in subset: Arabidopsis
in subset: Maize
in subset: Poaceae
in subset: Rice
in subset: TraitNet
comment: Often bears leaves and branches. In vascular plants, has at least one node and one internode.

Axiom
annotated source: shoot axis
annotated property: definition
annotated target: A plant axis (PO:0025004) that is part of a shoot system (PO:0009006).
has db xref: POC:curators

Axiom
annotated source: shoot axis
annotated property: has_exact_synonym
annotated target: eje del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot axis
annotated property: has_exact_synonym
annotated target: シュート軸 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

leaf
type: Class
subclass of: phyllome
definition: A phyllome (PO:0006001) that is not associated with a reproductive structure.
created by: rwalls
creation date: 2010-07-12T01:31:44Z
has db xref: PO_GIT:274
has db xref: PO_GIT:301
has_exact_synonym: hoja (Spanish, exact)
has_exact_synonym: 葉 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025034
in subset: TraitNet

Axiom
annotated source: leaf
annotated property: definition
annotated target: A phyllome (PO:0006001) that is not associated with a reproductive structure.
has db xref: POC:curators

Axiom
annotated source: leaf
annotated property: has_exact_synonym
annotated target: hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: leaf
annotated property: has_exact_synonym
annotated target: 葉 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

portion of ground tissue
type: Class
subclass of: portion of plant tissue
subclass of: anatomical entity
subclass of: Restriction
  on property: develops_from
  some values from: ground meristem
definition: Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).
created by: Laurel_Cooper
creation date: 2009-12-17T03:06:13Z
has db xref: PO_GIT:106
has_exact_synonym: fundamental tissue (exact)
has_exact_synonym: porci&#243n del tejido fundamental (Spanish, exact)
has_exact_synonym: 基本組織の一部 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025059
in subset: TraitNet
comment: Develops from the ground meristem (PO:0025594).

Axiom
annotated source: portion of ground tissue
annotated property: definition
annotated target: Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).
has db xref: ISBN:0471244554
has db xref: ISBN:0716710072

Axiom
annotated source: portion of ground tissue
annotated property: has_exact_synonym
annotated target: fundamental tissue (exact)
has db xref: ISBN:0471244554

Axiom
annotated source: portion of ground tissue
annotated property: has_exact_synonym
annotated target: porci&#243n del tejido fundamental (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: portion of ground tissue
annotated property: has_exact_synonym
annotated target: 基本組織の一部 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

lamina
type: Class
subclass of: cardinal part of multi-tissue plant structure
definition: A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat.
created by: Laurel_Cooper
creation date: 2009-12-18T11:23:59Z
has db xref: PO_GIT:428
has db xref: PO_GIT:70
has_exact_synonym: blade (exact)
has_exact_synonym: l&#225mina (Spanish, exact)
has_exact_synonym: laminae (exact, plural)
has_exact_synonym: 葉身、葉片 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025060
in subset: TraitNet
comment: PATO:0000407 (flat) and PATO:0000592 (thin).

Axiom
annotated source: lamina
annotated property: definition
annotated target: A cardinal part of multi-tissue plant structure (PO:0025498) that is thin and flat.
has db xref: POC:curators

Axiom
annotated source: lamina
annotated property: has_exact_synonym
annotated target: blade (exact)

Axiom
annotated source: lamina
annotated property: has_exact_synonym
annotated target: l&#225mina (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: lamina
annotated property: has_exact_synonym
annotated target: laminae (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: lamina
annotated property: has_exact_synonym
annotated target: 葉身、葉片 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

stalk
type: Class
subclass of: cardinal organ part
definition: A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part.
created by: Laurel_Cooper
creation date: 2009-12-18T10:09:17Z
has db xref: PATO:0001873
has db xref: PATO:0002226
has db xref: PO_GIT:52
has db xref: PO_GIT:78
has_exact_synonym: tallo de alto orden (secundario, terciario, etc) (Spanish, exact)
has_exact_synonym: 柄 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: stipe (related)
id: PO:0025066
in subset: TraitNet
comment: Some stalks may be ridged or grooved.

Axiom
annotated source: stalk
annotated property: definition
annotated target: A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part.
has db xref: POC:curators

Axiom
annotated source: stalk
annotated property: has_exact_synonym
annotated target: tallo de alto orden (secundario, terciario, etc) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stalk
annotated property: has_exact_synonym
annotated target: 柄 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: stalk
annotated property: has_related_synonym
annotated target: stipe (related)

branch
type: Class
subclass of: shoot axis
definition: A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
created by: rwalls
creation date: 2010-07-01T04:21:46Z
has db xref: PO_GIT:134
has_exact_synonym: ramificaci&#243n (Spanish, exact)
has_exact_synonym: shoot axis branch (exact)
has_exact_synonym: 枝 (Japanese, exact)
has narrow synonym: branchlet (narrow)
has narrow synonym: higher order axis (narrow)
has narrow synonym: secondary axis (narrow)
has narrow synonym: tertiary axis (narrow)
has narrow synonym: twig (narrow)
has OBO namespace: plant_anatomy
has_related_synonym: stem
has_related_synonym: twig
id: PO:0025073
in subset: TraitNet
comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.

Axiom
annotated source: branch
annotated property: definition
annotated target: A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).
has db xref: POC:curators

Axiom
annotated source: branch
annotated property: has_exact_synonym
annotated target: ramificaci&#243n (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: branch
annotated property: has_exact_synonym
annotated target: shoot axis branch (exact)
has db xref: POC:curators

Axiom
annotated source: branch
annotated property: has_exact_synonym
annotated target: 枝 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: branch
annotated property: hasNarrowSynonym
annotated target: branchlet (narrow)

reproductive shoot system
type: Class
subclass of: shoot system
subclass of: Restriction
  on property: participates in
  some values from: reproductive shoot system development stage
definition: A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
created by: rwalls
creation date: 2010-09-17T09:49:10Z
has_exact_synonym: sistema de brote reproductivo (Spanish, exact)
has_exact_synonym: 生殖シュート 系、苗条系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025082
in subset: TraitNet

Axiom
annotated source: reproductive shoot system
annotated property: definition
annotated target: A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094).
has db xref: POC:curators

Axiom
annotated source: reproductive shoot system
annotated property: has_exact_synonym
annotated target: sistema de brote reproductivo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: reproductive shoot system
annotated property: has_exact_synonym
annotated target: 生殖シュート 系、苗条系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

dehiscence zone
type: Class
subclass of: portion of plant tissue
definition: A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.
created by: rwalls
creation date: 2010-10-27T11:07:17Z
has db xref: GO:0009900
has_exact_synonym: zona de dehiscencia (Spanish, exact)
has_exact_synonym: 裂開帯 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025092

Axiom
annotated source: dehiscence zone
annotated property: definition
annotated target: A portion of plant tissue (PO:0009007) that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.
has db xref: POC:curators

Axiom
annotated source: dehiscence zone
annotated property: has_exact_synonym
annotated target: zona de dehiscencia (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: dehiscence zone
annotated property: has_exact_synonym
annotated target: 裂開帯 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant anatomical space
type: Class
subclass of: plant anatomical entity
definition: An anatomical space that is part of a plant.
created by: rwalls
creation date: 2010-11-10T11:57:16Z
has db xref: PO_GIT:203
has_exact_synonym: espacio anat&#243mico vegetal (Spanish, exact)
has_exact_synonym: 植物 解剖学（形態）的空間 (Japanese, exact)
has narrow synonym: lacuna (narrow)
has narrow synonym: lacunae (narrow, plural)
has narrow synonym: lumen (narrow)
has narrow synonym: lumina (narrow, plural)
has OBO namespace: plant_anatomy
id: PO:0025117
comment: CARO:0000005 'anatomical space' is defined as: An immaterial anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes, and is bounded by an anatomical surface.

Axiom
annotated source: plant anatomical space
annotated property: definition
annotated target: An anatomical space that is part of a plant.
has db xref: CARO:0000005
has db xref: PO:cooperl
has db xref: POC:curators

Axiom
annotated source: plant anatomical space
annotated property: has_exact_synonym
annotated target: espacio anat&#243mico vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant anatomical space
annotated property: has_exact_synonym
annotated target: 植物 解剖学（形態）的空間 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: plant anatomical space
annotated property: hasNarrowSynonym
annotated target: lacuna (narrow)

Axiom
annotated source: plant anatomical space
annotated property: hasNarrowSynonym
annotated target: lacunae (narrow, plural)
has synonym type: OMO_0003004

Axiom
annotated source: plant anatomical space
annotated property: hasNarrowSynonym
annotated target: lumen (narrow)

Axiom
annotated source: plant anatomical space
annotated property: hasNarrowSynonym
annotated target: lumina (narrow, plural)
has synonym type: OMO_0003004

primordium
type: Class
subclass of: portion of meristem tissue
definition: A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
created by: rwalls
creation date: 2010-11-15T09:10:22Z
has db xref: PO_GIT:186
has_exact_synonym: portion of primordial tissue (exact)
has_exact_synonym: portion of primordium tissue (exact)
has_exact_synonym: primordia (exact, plural)
has_exact_synonym: primordio (Spanish, exact)
has_exact_synonym: 原基（可視的） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025127
comment: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition.

Axiom
annotated source: primordium
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011).
has db xref: POC:curators

Axiom
annotated source: primordium
annotated property: has_exact_synonym
annotated target: primordia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: primordium
annotated property: has_exact_synonym
annotated target: primordio (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: primordium
annotated property: has_exact_synonym
annotated target: 原基（可視的） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome primordium
type: Class
subclass of: primordium
subclass of: anatomical entity
subclass of: Restriction
  on property: part of
  some values from: shoot axis apex
subclass of: Restriction
  on property: develops_from
  some values from: phyllome anlagen
definition: A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
created by: rwalls
creation date: 2010-11-15T09:27:11Z
has db xref: PO_GIT:466
has_exact_synonym: phyllome primordia (exact, plural)
has_exact_synonym: portion of phyllome primordium tissue (exact)
has_exact_synonym: primordio del filoma (Spanish, exact)
has_exact_synonym: フィロム原基（可視的） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025128
comment: The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop.

Axiom
annotated source: phyllome primordium
annotated property: definition
annotated target: A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001).
has db xref: PMID:11572953
has db xref: POC:curators

Axiom
annotated source: phyllome primordium
annotated property: has_exact_synonym
annotated target: phyllome primordia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: phyllome primordium
annotated property: has_exact_synonym
annotated target: primordio del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome primordium
annotated property: has_exact_synonym
annotated target: フィロム原基（可視的） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

petiole lamina
type: Class
equivalent class: Class
  intersection of: lamina
  intersection of: Restriction
    on property: part of
    some values from: petiole
subclass of: phyllome lamina
subclass of: Restriction
  on property: part of
  some values from: petiole
definition: A lamina (PO:0025060) that is part of a petiole (PO:0020038).
created by: rwalls
creation date: 2010-11-15T10:28:38Z
has db xref: PO_GIT:428
has_exact_synonym: l&#225mina (ala) del pec&#237olo (Spanish, exact)
has_exact_synonym: 葉柄葉身、葉片 (Japanese, exact)
has narrow synonym: petiole wing (narrow)
has OBO namespace: plant_anatomy
id: PO:0025129
in subset: Musa
comment: The entire petiole may be laminar, or the petiole may be more or less rounded in cross section with laminar extensions.

Axiom
annotated source: petiole lamina
annotated property: definition
annotated target: A lamina (PO:0025060) that is part of a petiole (PO:0020038).
has db xref: POC:curators

Axiom
annotated source: petiole lamina
annotated property: has_exact_synonym
annotated target: l&#225mina (ala) del pec&#237olo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: petiole lamina
annotated property: has_exact_synonym
annotated target: 葉柄葉身、葉片 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: petiole lamina
annotated property: hasNarrowSynonym
annotated target: petiole wing (narrow)
has db xref: CO_125:0000005

plant anatomical entity
type: Class
subclass of: material entity
subclass of: Restriction
definition: An anatomical entity that is or was part of a plant.
created by: rwalls
creation date: 2010-11-15T11:41:38Z
has db xref: PO_GIT:224
has_exact_synonym: entidad anat&#243mica vegetal (Spanish, exact)
has_exact_synonym: 植物 解剖学（形態）的実体 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025131
comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.

Axiom
annotated source: plant anatomical entity
annotated property: subClassOf
annotated target: Restriction
source: cjm

Axiom
annotated source: plant anatomical entity
annotated property: definition
annotated target: An anatomical entity that is or was part of a plant.
has db xref: BFO:0000004
has db xref: CARO:0000000
has db xref: CAROC:Brownsville2014
has db xref: POC:curators

Axiom
annotated source: plant anatomical entity
annotated property: has_exact_synonym
annotated target: entidad anat&#243mica vegetal (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant anatomical entity
annotated property: has_exact_synonym
annotated target: 植物 解剖学（形態）的実体 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome epidermis
type: Class
equivalent class: Class
  intersection of: shoot system epidermis
  intersection of: Restriction
    on property: part of
    some values from: phyllome
subclass of: shoot system epidermis
subclass of: Restriction
  on property: part of
  some values from: phyllome
definition: A portion of shoot system epidermis (PO:0006035) that is part of a phyllome (PO:0006001).
created by: rwalls
creation date: 2010-11-15T02:32:53Z
has_exact_synonym: epidermis del filoma (Spanish, exact)
has_exact_synonym: フィロム表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025157

Axiom
annotated source: phyllome epidermis
annotated property: definition
annotated target: A portion of shoot system epidermis (PO:0006035) that is part of a phyllome (PO:0006001).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: phyllome epidermis
annotated property: has_exact_synonym
annotated target: epidermis del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome epidermis
annotated property: has_exact_synonym
annotated target: フィロム表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

stem epidermis
type: Class
equivalent class: Class
  intersection of: shoot axis epidermis
  intersection of: Restriction
    on property: part of
    some values from: stem
subclass of: shoot axis epidermis
subclass of: Restriction
  on property: part of
  some values from: stem
definition: A portion of shoot axis epidermis (PO:0000112) that is part of a stem (PO:0009047).
created by: rwalls
creation date: 2010-11-22T09:56:21Z
has db xref: PO_GIT:111
has_exact_synonym: epidermis del tallo (Spanish, exact)
has_exact_synonym: 茎表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
has_related_synonym: culm epidermis (related)
id: PO:0025178

Axiom
annotated source: stem epidermis
annotated property: definition
annotated target: A portion of shoot axis epidermis (PO:0000112) that is part of a stem (PO:0009047).
has db xref: POC:Laurel_Cooper
has db xref: POC:Ramona_Walls

Axiom
annotated source: stem epidermis
annotated property: has_exact_synonym
annotated target: epidermis del tallo (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: stem epidermis
annotated property: has_exact_synonym
annotated target: 茎表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

branch epidermis
type: Class
equivalent class: Class
  intersection of: shoot axis epidermis
  intersection of: Restriction
    on property: part of
    some values from: branch
subclass of: shoot axis epidermis
subclass of: Restriction
  on property: part of
  some values from: branch
definition: A portion of shoot axis epidermis (PO:0006035) that is part of a branch (PO:0025073).
created by: rwalls
creation date: 2010-11-22T09:58:06Z
has_exact_synonym: epidermis de la ramificaci&#243n (Spanish, exact)
has_exact_synonym: 枝 表皮 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025179

Axiom
annotated source: branch epidermis
annotated property: definition
annotated target: A portion of shoot axis epidermis (PO:0006035) that is part of a branch (PO:0025073).
has db xref: POC:Ramona_Walls

Axiom
annotated source: branch epidermis
annotated property: has_exact_synonym
annotated target: epidermis de la ramificaci&#243n (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: branch epidermis
annotated property: has_exact_synonym
annotated target: 枝 表皮 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome trichome
type: Class
subclass of: trichome
definition: A trichome that is part of a phyllome epidermis.
created by: rwalls
creation date: 2010-12-06T01:17:31Z
has_exact_synonym: tricoma del filoma (Spanish, exact)
has_exact_synonym: フィロム毛（毛茸、糸状体） (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025186

Axiom
annotated source: phyllome trichome
annotated property: definition
annotated target: A trichome that is part of a phyllome epidermis.
has db xref: POC:Ramona_Walls

Axiom
annotated source: phyllome trichome
annotated property: has_exact_synonym
annotated target: tricoma del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome trichome
annotated property: has_exact_synonym
annotated target: フィロム毛（毛茸、糸状体） (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot system vascular system
type: Class
subclass of: vascular system
subclass of: Restriction
  on property: part of
  some values from: shoot system
definition: A vascular system (PO:0000034) that is part of a shoot system (PO:0009006).
created by: rwalls
creation date: 2010-12-17T09:34:58Z
has db xref: PO_GIT:41
has_exact_synonym: sistema vascular del sistema del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: シュート系維管系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025205

Axiom
annotated source: shoot system vascular system
annotated property: definition
annotated target: A vascular system (PO:0000034) that is part of a shoot system (PO:0009006).
has db xref: POC:Ramona_Walls

Axiom
annotated source: shoot system vascular system
annotated property: has_exact_synonym
annotated target: sistema vascular del sistema del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: shoot system vascular system
annotated property: has_exact_synonym
annotated target: シュート系維管系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome vascular system
type: Class
subclass of: vascular system
subclass of: Restriction
  on property: part of
  some values from: phyllome
subclass of: Restriction
  on property: part of
  some values from: shoot system vascular system
definition: A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a phyllome (PO:0006001).
created by: rwalls
creation date: 2010-12-17T10:11:07Z
has db xref: PO_GIT:41
has_exact_synonym: sistema vascular del filoma (Spanish, exact)
has_exact_synonym: フィロム維管系 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025206

Axiom
annotated source: phyllome vascular system
annotated property: has_exact_synonym
annotated target: フィロム維管系 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

Axiom
annotated source: phyllome vascular system
annotated property: definition
annotated target: A vascular system (PO:0000034) that includes the totality of the portions of vascular tissue in their specific arrangement in a phyllome (PO:0006001).
has db xref: POC:Ramona_Walls

Axiom
annotated source: phyllome vascular system
annotated property: has_exact_synonym
annotated target: sistema vascular del filoma (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

reproductive shoot apex
type: Class
subclass of: shoot axis apex
definition: A shoot apex that has as part a reproductive shoot apical meristem.
created by: rwalls
creation date: 2010-12-20T08:47:03Z
has_exact_synonym: &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: 生殖シュート頂、茎頂 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025222

Axiom
annotated source: reproductive shoot apex
annotated property: definition
annotated target: A shoot apex that has as part a reproductive shoot apical meristem.
has db xref: POC:Ramona_Walls

Axiom
annotated source: reproductive shoot apex
annotated property: has_exact_synonym
annotated target: &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: reproductive shoot apex
annotated property: has_exact_synonym
annotated target: 生殖シュート頂、茎頂 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

vegetative shoot apex
type: Class
subclass of: shoot axis apex
subclass of: Restriction
  on property: has part
  some values from: vegetative shoot apical meristem
definition: A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016).
created by: rwalls
creation date: 2010-12-20T08:47:03Z
has db xref: PO_GIT:234
has_exact_synonym: &#225pice vegetativo del epiblasto (epiblastema) (Spanish, exact)
has_exact_synonym: 栄養シュート頂、栄養枝頂 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025223

Axiom
annotated source: vegetative shoot apex
annotated property: definition
annotated target: A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016).
has db xref: POC:Laurel_Cooper
has db xref: POC:Ramona_Walls

Axiom
annotated source: vegetative shoot apex
annotated property: has_exact_synonym
annotated target: &#225pice vegetativo del epiblasto (epiblastema) (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: vegetative shoot apex
annotated property: has_exact_synonym
annotated target: 栄養シュート頂、栄養枝頂 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

axil
type: Class
subclass of: plant anatomical space
definition: A plant anatomical space that is the space between a shoot axis and a leaf, bract, or branch that branches from the shoot axis.
created by: rwalls
creation date: 2010-12-20T08:59:45Z
has_exact_synonym: axila (Spanish, exact)
has_exact_synonym: 腋、軸 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025224

Axiom
annotated source: axil
annotated property: definition
annotated target: A plant anatomical space that is the space between a shoot axis and a leaf, bract, or branch that branches from the shoot axis.
has db xref: POC:curators

Axiom
annotated source: axil
annotated property: has_exact_synonym
annotated target: axila (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: axil
annotated property: has_exact_synonym
annotated target: 腋、軸 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

life of whole plant stage
type: Class
subclass of: whole plant development stage
definition: A maximal whole plant development stage.
created by: rwalls
creation date: 2011-10-19T10:54:37Z
has db xref: PO_GIT:230
has_exact_synonym: vida de la planta entera (Spanish, exact)
has_exact_synonym: 植物体の一生 (Japanese, exact)
has OBO namespace: plant_structure_development_stage
id: PO:0025337
comment: There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.

Axiom
annotated source: life of whole plant stage
annotated property: definition
annotated target: A maximal whole plant development stage.
has db xref: POC:curators

Axiom
annotated source: life of whole plant stage
annotated property: has_exact_synonym
annotated target: vida de la planta entera (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: life of whole plant stage
annotated property: has_exact_synonym
annotated target: 植物体の一生 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

collective plant organ structure development stage
type: Class
subclass of: plant structure development stage
subclass of: Restriction
  on property: has participant
  some values from: collective plant organ structure
definition: A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
created by: rwalls
creation date: 2011-10-19T11:12:49Z
has db xref: PO_GIT:391
has_exact_synonym: etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
has_exact_synonym: 集合的植物構造の発生過程 (Japanese, exact)
has OBO namespace: plant_structure_development_stage
id: PO:0025338
comment: Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083).

Axiom
annotated source: collective plant organ structure development stage
annotated property: definition
annotated target: A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497).
has db xref: POC:curators

Axiom
annotated source: collective plant organ structure development stage
annotated property: has_exact_synonym
annotated target: etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: collective plant organ structure development stage
annotated property: has_exact_synonym
annotated target: 集合的植物構造の発生過程 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome lamina vein
type: Class
equivalent class: Class
  intersection of: vascular bundle
  intersection of: Restriction
    on property: part of
    some values from: phyllome lamina
subclass of: vascular bundle
subclass of: Restriction
  on property: part of
  some values from: phyllome lamina
definition: A vascular bundle (PO:0005020) that is part of a phyllome lamina (PO:0025396).
created by: rwalls
creation date: 2012-04-18T01:41:29Z
has db xref: PO_GIT:462
has_exact_synonym: vena del filoma laminar (Spanish, exact)
has_exact_synonym: フィロム葉身脈 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025348

Axiom
annotated source: phyllome lamina vein
annotated property: definition
annotated target: A vascular bundle (PO:0005020) that is part of a phyllome lamina (PO:0025396).
has db xref: POC:Ramona_Walls

Axiom
annotated source: phyllome lamina vein
annotated property: has_exact_synonym
annotated target: vena del filoma laminar (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome lamina vein
annotated property: has_exact_synonym
annotated target: フィロム葉身脈 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

floral organ
type: Class
equivalent class: Class
  intersection of: plant organ
  intersection of: Restriction
    on property: part of
    some values from: flower
subclass of: plant organ
subclass of: Restriction
  on property: part of
  some values from: flower
definition: A plant organ (PO:0009008) that is part of a flower (PO:0009046).
created by: rwalls
creation date: 2012-01-19T11:44:36Z
has db xref: PO_GIT:423
has_exact_synonym: &#243rgano floral (Spanish, exact)
has_exact_synonym: flower organ (exact)
has_exact_synonym: 花器官 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025395
comment: Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores.

Axiom
annotated source: floral organ
annotated property: definition
annotated target: A plant organ (PO:0009008) that is part of a flower (PO:0009046).
has db xref: POC:curators

Axiom
annotated source: floral organ
annotated property: has_exact_synonym
annotated target: &#243rgano floral (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: floral organ
annotated property: has_exact_synonym
annotated target: 花器官 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome lamina
type: Class
equivalent class: Class
  intersection of: plant organ lamina
  intersection of: Restriction
    on property: part of
    some values from: phyllome
subclass of: plant organ lamina
subclass of: Restriction
  on property: part of
  some values from: phyllome
definition: A plant organ lamina (PO:0025513) that is part of a phyllome (PO:0006001).
created by: rwalls
creation date: 2012-01-19T12:56:11Z
has db xref: PO_GIT:428
has_exact_synonym: filoma laminar (Spanish, exact)
has_exact_synonym: フィロム葉身 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025396

Axiom
annotated source: phyllome lamina
annotated property: definition
annotated target: A plant organ lamina (PO:0025513) that is part of a phyllome (PO:0006001).
has db xref: POC:Ramona_Walls

Axiom
annotated source: phyllome lamina
annotated property: has_exact_synonym
annotated target: filoma laminar (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: phyllome lamina
annotated property: has_exact_synonym
annotated target: フィロム葉身 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

primary leaf vein
type: Class
subclass of: leaf lamina vein
definition: A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
created by: rwalls
creation date: 2012-02-01T04:24:58Z
has db xref: PO_GIT:435
has_exact_synonym: vena primaria de la hoja (Spanish, exact)
has_exact_synonym: 一次葉脈 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025413
comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as found in some ferns and gymnosperms.

Axiom
annotated source: primary leaf vein
annotated property: definition
annotated target: A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
has db xref: POC:curators

Axiom
annotated source: primary leaf vein
annotated property: has_exact_synonym
annotated target: vena primaria de la hoja (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: primary leaf vein
annotated property: has_exact_synonym
annotated target: 一次葉脈 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

phyllome anlagen
type: Class
subclass of: portion of meristem tissue
subclass of: Restriction
  on property: part of
  some values from: peripheral zone
definition: A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
created by: Laurel_Cooper
creation date: 2012-02-07T08:20:10Z
has broad synonym: phyllome meristem (broad)
has db xref: PO_GIT:427
has_exact_synonym: フィロム原基 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025430
comment: The phyllome anlagen is only detectable by gene expression, not morphology.

Axiom
annotated source: phyllome anlagen
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

Axiom
annotated source: phyllome anlagen
annotated property: has_exact_synonym
annotated target: フィロム原基 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

vascular leaf anlagen
type: Class
subclass of: phyllome anlagen
subclass of: Restriction
  on property: part of
  some values from: vegetative shoot apical meristem
definition: A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148).
created by: Laurel_Cooper
creation date: 2012-02-07T08:40:37Z
has broad synonym: leaf meristem (broad)
has db xref: PO_GIT:407
has_exact_synonym: 維管束系葉原基 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025431
comment: This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied).

Axiom
annotated source: vascular leaf anlagen
annotated property: definition
annotated target: A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148).
has db xref: PMID:14732442
has db xref: POC:Laurel_Cooper

Axiom
annotated source: vascular leaf anlagen
annotated property: has_exact_synonym
annotated target: 維管束系葉原基 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

root anlagen
type: Class
subclass of: portion of meristem tissue
definition: A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
created by: Laurel_Cooper
creation date: 2012-02-08T01:00:56Z
has db xref: PO_GIT:427
has_exact_synonym: precursor de ra&#237 (Spanish, exact)
has_exact_synonym: 根原基 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025433
comment: Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).

Axiom
annotated source: root anlagen
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029).
has db xref: POC:curators

Axiom
annotated source: root anlagen
annotated property: has_exact_synonym
annotated target: precursor de ra&#237 (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: root anlagen
annotated property: has_exact_synonym
annotated target: 根原基 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

floral organ primordium
type: Class
subclass of: primordium
subclass of: Restriction
  on property: part of
  some values from: reproductive shoot apex
definition: A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
created by: rwalls
creation date: 2012-04-26T03:57:09Z
has db xref: PO_GIT:465
has_exact_synonym: floral structure primordia (exact, plural)
has_exact_synonym: portion of floral structure primordium tissue (exact)
has_exact_synonym: primordio de organo floral (Spanish, exact)
has_exact_synonym: 花器官原基 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025477
in subset: Angiosperm
comment: If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089).

Axiom
annotated source: floral organ primordium
annotated property: definition
annotated target: A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222).
has db xref: POC:curators

Axiom
annotated source: floral organ primordium
annotated property: has_exact_synonym
annotated target: floral structure primordia (exact, plural)
has synonym type: OMO_0003004

Axiom
annotated source: floral organ primordium
annotated property: has_exact_synonym
annotated target: primordio de organo floral (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: floral organ primordium
annotated property: has_exact_synonym
annotated target: 花器官原基 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

multi-tissue plant structure
type: Class
subclass of: plant structure
definition: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
created by: Laurel_Cooper
creation date: 2012-06-11T14:57:00Z
has db xref: PO_GIT:480
has_exact_synonym: estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
has_exact_synonym: 複数の組織からなる植物構造 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025496
comment: Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types.

Axiom
annotated source: multi-tissue plant structure
annotated property: definition
annotated target: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types.
has db xref: CARO:0000055
has db xref: POC:curators

Axiom
annotated source: multi-tissue plant structure
annotated property: has_exact_synonym
annotated target: estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: multi-tissue plant structure
annotated property: has_exact_synonym
annotated target: 複数の組織からなる植物構造 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

collective plant structure
type: Class
subclass of: plant structure
definition: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
created by: Laurel_Cooper
creation date: 2012-06-11T15:09:20Z
has db xref: PO_GIT:479
has_exact_synonym: estructura vegetal colectiva (Spanish, exact)
has_exact_synonym: 集合的植物構造 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025497
comment: This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006).

Axiom
annotated source: collective plant structure
annotated property: definition
annotated target: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).
has db xref: POC:curators

Axiom
annotated source: collective plant structure
annotated property: has_exact_synonym
annotated target: estructura vegetal colectiva (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: collective plant structure
annotated property: has_exact_synonym
annotated target: 集合的植物構造 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

cardinal part of multi-tissue plant structure
type: Class
subclass of: plant structure
subclass of: Restriction
  on property: part of
  some values from: multi-tissue plant structure
definition: A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.
created by: Laurel_Cooper
creation date: 2012-06-11T15:28:44Z
has db xref: PO_GIT:485
has_exact_synonym: parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
has_exact_synonym: 複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025498
comment: Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049).

Axiom
annotated source: cardinal part of multi-tissue plant structure
annotated property: definition
annotated target: A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.
has db xref: POC:curators

Axiom
annotated source: cardinal part of multi-tissue plant structure
annotated property: has_exact_synonym
annotated target: parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: cardinal part of multi-tissue plant structure
annotated property: has_exact_synonym
annotated target: 複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

plant organ lamina
type: Class
equivalent class: Class
  intersection of: lamina
  intersection of: Restriction
    on property: part of
    some values from: plant organ
subclass of: cardinal organ part
subclass of: lamina
definition: A lamina (PO:0025060) that is part of a plant organ (PO:0009008).
created by: rwalls
creation date: 2012-10-17T15:51:02Z
has db xref: PO_GIT:428
has_exact_synonym: lámina órgano (Spanish, exact)
has_exact_synonym: 器官 葉身 (Japanese, exact)
has OBO namespace: plant_anatomy
id: PO:0025513

Axiom
annotated source: plant organ lamina
annotated property: definition
annotated target: A lamina (PO:0025060) that is part of a plant organ (PO:0009008).
has db xref: POC:curators

Axiom
annotated source: plant organ lamina
annotated property: has_exact_synonym
annotated target: lámina órgano (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: plant organ lamina
annotated property: has_exact_synonym
annotated target: 器官 葉身 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

shoot system development stage
type: Class
subclass of: collective plant organ structure development stage
subclass of: Restriction
  on property: has participant
  some values from: shoot system
definition: A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
created by: Laurel_Cooper
creation date: 2012-12-13T18:21:19Z
has db xref: PO_GIT:517
has OBO namespace: plant_structure_development_stage
id: PO:0025527
comment: The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003).

Axiom
annotated source: shoot system development stage
annotated property: definition
annotated target: A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.
has db xref: POC:Laurel_Cooper

bud development stage
type: Class
subclass of: shoot system development stage
definition: A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).
created by: Laurel_Cooper
creation date: 2012-12-13T18:29:35Z
has db xref: PO_GIT:517
has OBO namespace: plant_structure_development_stage
id: PO:0025528

Axiom
annotated source: bud development stage
annotated property: definition
annotated target: A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).
has db xref: POC:Laurel_Cooper

reproductive shoot system development stage
type: Class
subclass of: shoot system development stage
definition: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
created by: Laurel_Cooper
creation date: 2012-12-13T19:01:14Z
has db xref: PO_GIT:517
has OBO namespace: plant_structure_development_stage
id: PO:0025530

Axiom
annotated source: reproductive shoot system development stage
annotated property: definition
annotated target: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
has db xref: POC:Laurel_Cooper

ground meristem
type: Class
subclass of: portion of meristem tissue
definition: A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
created by: Laurel_Cooper
creation date: 2013-11-18T11:14:03Z
has db xref: PO_GIT:584
has OBO namespace: plant_anatomy
id: PO:0025594

Axiom
annotated source: ground meristem
annotated property: definition
annotated target: A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
has db xref: POC:Laurel_Cooper
has db xref: POC:curators

native plant cell
type: Class
subclass of: plant cell
definition: A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
created by: Laurel_Cooper
creation date: 2014-05-13T16:51:47Z
has db xref: PO_GIT:586
has OBO namespace: plant_anatomy
id: PO:0025606
comment: A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004).

Axiom
annotated source: native plant cell
annotated property: definition
annotated target: A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment).
has db xref: POC:Laurel_Cooper

sporophyte development stage
type: Class
subclass of: whole plant development stage
subclass of: Restriction
  on property: part of
  some values from: life of whole plant stage
definition: A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
created by: rwalls
creation date: 2010-07-15T02:56:11Z
has db xref: PO_GIT:139
has db xref: PO_GIT:68
has_exact_synonym: fase esporof&#237tica (Spanish, exact)
has_exact_synonym: sporophytic development stage (exact)
has_exact_synonym: sporophytic phase (exact)
has_exact_synonym: sporphyte phase (exact)
has_exact_synonym: 胞子体発生過程 (Japanese, exact)
has OBO namespace: plant_structure_development_stage
id: PO:0028002
in subset: TraitNet
comment: A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis.

Axiom
annotated source: sporophyte development stage
annotated property: definition
annotated target: A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
has db xref: POC:curators

Axiom
annotated source: sporophyte development stage
annotated property: has_exact_synonym
annotated target: fase esporof&#237tica (Spanish, exact)
has db xref: POC:Maria_Alejandra_Gandolfo
has synonym type: Spanish

Axiom
annotated source: sporophyte development stage
annotated property: has_exact_synonym
annotated target: 胞子体発生過程 (Japanese, exact)
has db xref: NIG:Yukiko_Yamazaki
has synonym type: Japanese

catkin inflorescence
type: Class
subclass of: inflorescence
definition: An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of indeterminate, first order inflorescence axes (PO:0025104) and sessile, unisexual flowers (PO:0009046) that are each subtended by conspicuous inflorescence bracts (PO:0009054).
created by: NYBG:Brandon_Sinn
creation date: 2017-04-20T12:48:27Z
has_exact_synonym: ament
has_exact_synonym: ament (exact)
has_exact_synonym: catkin
has_exact_synonym: catkin (exact)
has OBO namespace: plant_anatomy
id: PO:0030119
comment: Examples include poplars (including Populus trichocarpa, Salicaceae) and birches (Betula spp., Betulaceae). Catkin inflorescences are often pendulate.

Axiom
annotated source: catkin inflorescence
annotated property: definition
annotated target: An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of indeterminate, first order inflorescence axes (PO:0025104) and sessile, unisexual flowers (PO:0009046) that are each subtended by conspicuous inflorescence bracts (PO:0009054).
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has db xref: PO:cooperl

capitulum inflorescence
type: Class
subclass of: inflorescence
definition: An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of a radially-enlarged, determinate, first order inflorescence axis (PO:0025104) with sessile flowers (PO:0009046).
created by: NYBG:Brandon_Sinn
creation date: 2017-04-20T12:53:49Z
has broad synonym: head (broad)
has_exact_synonym: calathidium (exact)
has_exact_synonym: capitula (exact, plural)
has_exact_synonym: capitulum (exact)
has narrow synonym: hypanthodium (narrow)
has OBO namespace: plant_anatomy
id: PO:0030121
comment: Many capitulum inflorescences have basal involucral bracts (PO:0009045) and are often discoid or globose in shape. Examples include sunflowers (Helianthus spp.; Asteraceae) and teasels (Dipsacus spp.; Dipsacaceae).

Axiom
annotated source: capitulum inflorescence
annotated property: definition
annotated target: An inflorescence (PO:0009049) with a monopodial growth habit, which at flowering stage (PO:0007616) is composed of a radially-enlarged, determinate, first order inflorescence axis (PO:0025104) with sessile flowers (PO:0009046).
has db xref: NYBG:Brandon_Sinn
has db xref: NYBG:Dario_Cavaliere
has db xref: PO:cooperl

Axiom
annotated source: capitulum inflorescence
annotated property: has_exact_synonym
annotated target: capitula (exact, plural)
has synonym type: OMO_0003004

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.

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

abscission zone
type: Class
subclass of: portion of plant tissue

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

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

organizational term
type: NamedIndividual
IAO_0000111: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

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

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

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

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

to be replaced with external ontology term
type: NamedIndividual
IAO_0000111: to be replaced with external ontology term
definition: 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
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

winter
type: NamedIndividual
type: season

spring
type: NamedIndividual
type: season

summer
type: NamedIndividual
type: season

autumn
type: NamedIndividual
type: season

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: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  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: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

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: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x